Starting phenix.real_space_refine on Thu Feb 15 02:43:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph2_13404/02_2024/7ph2_13404_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph2_13404/02_2024/7ph2_13404.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph2_13404/02_2024/7ph2_13404_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph2_13404/02_2024/7ph2_13404_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph2_13404/02_2024/7ph2_13404_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph2_13404/02_2024/7ph2_13404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph2_13404/02_2024/7ph2_13404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph2_13404/02_2024/7ph2_13404_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ph2_13404/02_2024/7ph2_13404_updated.pdb" } resolution = 3.7 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= 0.002 sd= 0.046 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: 6 Type Number sf(0) Gaussians Gd 2 15.26 5 P 2 5.49 5 S 64 5.16 5 C 6754 2.51 5 N 1834 2.21 5 O 2032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 56": "NH1" <-> "NH2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10688 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4388 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 555} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 4388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4388 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 555} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 836 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 850 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 150 Unusual residues: {'EIW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Ad-hoc single atom residues: {' GD': 1} Unusual residues: {'88T': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Ad-hoc single atom residues: {' GD': 1} Unusual residues: {'88T': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C10 88T C 200 " occ=0.09 ... (35 atoms not shown) pdb=" O9 88T C 200 " occ=0.09 residue: pdb=" C10 88T D 200 " occ=0.09 ... (35 atoms not shown) pdb=" O9 88T D 200 " occ=0.09 Time building chain proxies: 5.90, per 1000 atoms: 0.55 Number of scatterers: 10688 At special positions: 0 Unit cell: (99.603, 97.092, 162.378, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Gd 2 63.96 S 64 16.00 P 2 15.00 O 2032 8.00 N 1834 7.00 C 6754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.05 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 2.1 seconds 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2524 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 6 sheets defined 49.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.61 Creating SS restraints... Processing helix chain 'A' and resid 13 through 16 Processing helix chain 'A' and resid 18 through 57 Proline residue: A 22 - end of helix removed outlier: 4.977A pdb=" N ALA A 25 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A 26 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 27 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 35 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A 36 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 37 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 40 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 44 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Proline residue: A 50 - end of helix removed outlier: 3.824A pdb=" N ASP A 53 " --> pdb=" O PRO A 50 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ASP A 54 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY A 55 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 56 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 57 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 106 removed outlier: 4.177A pdb=" N ILE A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A 92 " --> pdb=" O CYS A 88 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 123 through 161 removed outlier: 3.604A pdb=" N ALA A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 192 Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 224 through 249 removed outlier: 3.924A pdb=" N ARG A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 269 removed outlier: 3.737A pdb=" N LEU A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 322 removed outlier: 3.665A pdb=" N MET A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.738A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 removed outlier: 4.091A pdb=" N ASN A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 436 No H-bonds generated for 'chain 'A' and resid 433 through 436' Processing helix chain 'A' and resid 447 through 456 removed outlier: 3.753A pdb=" N GLU A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 483 through 497 removed outlier: 3.511A pdb=" N GLN A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.565A pdb=" N LYS A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 563 through 566 No H-bonds generated for 'chain 'A' and resid 563 through 566' Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.967A pdb=" N MET A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 53 Proline residue: B 18 - end of helix Proline residue: B 22 - end of helix removed outlier: 4.938A pdb=" N ALA B 25 " --> pdb=" O PRO B 22 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 35 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 36 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER B 40 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 65 through 90 removed outlier: 4.748A pdb=" N LEU B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 70 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 removed outlier: 4.477A pdb=" N THR B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 116 Processing helix chain 'B' and resid 122 through 163 removed outlier: 3.564A pdb=" N LEU B 125 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR B 130 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP B 131 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ARG B 148 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU B 149 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 153 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 154 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR B 162 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 212 Proline residue: B 176 - end of helix removed outlier: 4.646A pdb=" N ASN B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N MET B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 removed outlier: 4.070A pdb=" N PHE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 250 removed outlier: 4.224A pdb=" N LYS B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 269 removed outlier: 4.167A pdb=" N LEU B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.888A pdb=" N THR B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 322 removed outlier: 3.973A pdb=" N THR B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASN B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.716A pdb=" N ALA B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 456 removed outlier: 3.624A pdb=" N GLU B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 No H-bonds generated for 'chain 'B' and resid 460 through 463' Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 483 through 497 removed outlier: 3.584A pdb=" N LEU B 496 " --> pdb=" O ALA B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 526 Processing helix chain 'B' and resid 539 through 543 Processing helix chain 'B' and resid 562 through 565 No H-bonds generated for 'chain 'B' and resid 562 through 565' Processing helix chain 'B' and resid 573 through 576 No H-bonds generated for 'chain 'B' and resid 573 through 576' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing sheet with id= A, first strand: chain 'A' and resid 547 through 549 removed outlier: 3.617A pdb=" N GLU A 547 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 373 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER A 532 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU A 374 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL A 534 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU A 502 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 532 through 535 removed outlier: 6.815A pdb=" N GLU B 547 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL B 375 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 549 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= D, first strand: chain 'C' and resid 108 through 110 removed outlier: 5.479A pdb=" N ARG C 38 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASN C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.792A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 108 through 110 removed outlier: 3.832A pdb=" N TYR D 93 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA D 91 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG D 38 " --> pdb=" O ASN D 47 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 4161 1.39 - 1.60: 6570 1.60 - 1.82: 121 1.82 - 2.04: 1 2.04 - 2.25: 1 Bond restraints: 10854 Sorted by residual: bond pdb=" O6 88T C 200 " pdb=" O9 88T C 200 " ideal model delta sigma weight residual 1.419 2.253 -0.834 2.00e-02 2.50e+03 1.74e+03 bond pdb=" O4 88T C 200 " pdb=" O8 88T C 200 " ideal model delta sigma weight residual 1.405 1.794 -0.389 2.00e-02 2.50e+03 3.78e+02 bond pdb=" C11 88T C 200 " pdb=" N4 88T C 200 " ideal model delta sigma weight residual 1.837 1.488 0.349 2.00e-02 2.50e+03 3.05e+02 bond pdb=" C11 88T D 200 " pdb=" N4 88T D 200 " ideal model delta sigma weight residual 1.837 1.491 0.346 2.00e-02 2.50e+03 3.00e+02 bond pdb=" C12 88T D 200 " pdb=" N4 88T D 200 " ideal model delta sigma weight residual 1.814 1.492 0.322 2.00e-02 2.50e+03 2.60e+02 ... (remaining 10849 not shown) Histogram of bond angle deviations from ideal: 82.07 - 99.07: 4 99.07 - 116.07: 7266 116.07 - 133.07: 7384 133.07 - 150.07: 15 150.07 - 167.08: 1 Bond angle restraints: 14670 Sorted by residual: angle pdb=" C10 88T D 200 " pdb=" O4 88T D 200 " pdb=" O8 88T D 200 " ideal model delta sigma weight residual 109.57 167.08 -57.51 3.00e+00 1.11e-01 3.67e+02 angle pdb=" C10 88T C 200 " pdb=" O4 88T C 200 " pdb=" O8 88T C 200 " ideal model delta sigma weight residual 109.57 148.27 -38.70 3.00e+00 1.11e-01 1.66e+02 angle pdb=" C21 88T D 200 " pdb=" O8 88T D 200 " pdb=" O4 88T D 200 " ideal model delta sigma weight residual 105.77 143.52 -37.75 3.00e+00 1.11e-01 1.58e+02 angle pdb=" C15 88T C 200 " pdb=" O6 88T C 200 " pdb=" O9 88T C 200 " ideal model delta sigma weight residual 109.36 140.99 -31.63 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C PRO A 297 " pdb=" CA PRO A 297 " pdb=" CB PRO A 297 " ideal model delta sigma weight residual 111.56 94.58 16.98 1.65e+00 3.67e-01 1.06e+02 ... (remaining 14665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 6434 35.92 - 71.84: 132 71.84 - 107.76: 24 107.76 - 143.68: 17 143.68 - 179.60: 6 Dihedral angle restraints: 6613 sinusoidal: 2693 harmonic: 3920 Sorted by residual: dihedral pdb=" C PRO A 297 " pdb=" N PRO A 297 " pdb=" CA PRO A 297 " pdb=" CB PRO A 297 " ideal model delta harmonic sigma weight residual -120.70 -102.46 -18.24 0 2.50e+00 1.60e-01 5.32e+01 dihedral pdb=" C ARG A 296 " pdb=" N ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta harmonic sigma weight residual -122.60 -104.60 -18.00 0 2.50e+00 1.60e-01 5.19e+01 dihedral pdb=" C TYR A 393 " pdb=" N TYR A 393 " pdb=" CA TYR A 393 " pdb=" CB TYR A 393 " ideal model delta harmonic sigma weight residual -122.60 -105.43 -17.17 0 2.50e+00 1.60e-01 4.72e+01 ... (remaining 6610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.393: 1725 1.393 - 2.786: 0 2.786 - 4.180: 0 4.180 - 5.573: 3 5.573 - 6.966: 2 Chirality restraints: 1730 Sorted by residual: chirality pdb=" N4 88T D 200 " pdb=" C11 88T D 200 " pdb=" C12 88T D 200 " pdb=" C22 88T D 200 " both_signs ideal model delta sigma weight residual False 4.34 -2.63 6.97 2.00e-01 2.50e+01 1.21e+03 chirality pdb=" N4 88T C 200 " pdb=" C11 88T C 200 " pdb=" C12 88T C 200 " pdb=" C22 88T C 200 " both_signs ideal model delta sigma weight residual False 4.34 -2.59 6.93 2.00e-01 2.50e+01 1.20e+03 chirality pdb=" C42 EIW A 601 " pdb=" C43 EIW A 601 " pdb=" C46 EIW A 601 " pdb=" O71 EIW A 601 " both_signs ideal model delta sigma weight residual False 2.54 -2.59 5.13 2.00e-01 2.50e+01 6.58e+02 ... (remaining 1727 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 148 " 0.484 9.50e-02 1.11e+02 2.17e-01 2.87e+01 pdb=" NE ARG A 148 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 148 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 148 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 148 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 322 " -0.023 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C LEU A 322 " 0.081 2.00e-02 2.50e+03 pdb=" O LEU A 322 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP A 323 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 578 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C MET B 578 " 0.079 2.00e-02 2.50e+03 pdb=" O MET B 578 " -0.029 2.00e-02 2.50e+03 pdb=" N GLN B 579 " -0.027 2.00e-02 2.50e+03 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 243 2.66 - 3.22: 10847 3.22 - 3.78: 15497 3.78 - 4.34: 21506 4.34 - 4.90: 34457 Nonbonded interactions: 82550 Sorted by model distance: nonbonded pdb=" O ASP A 60 " pdb=" OD1 ASP A 60 " model vdw 2.104 3.040 nonbonded pdb=" O ASP B 117 " pdb=" OD1 ASP B 117 " model vdw 2.212 3.040 nonbonded pdb=" O HIS B 107 " pdb=" ND1 HIS B 107 " model vdw 2.224 2.520 nonbonded pdb=" O8 88T D 200 " pdb="GD GD D 201 " model vdw 2.247 3.310 nonbonded pdb=" O6 88T C 200 " pdb="GD GD C 201 " model vdw 2.247 3.310 ... (remaining 82545 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' and resid 12 through 580) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 1 through 111 or resid 200 through 201)) } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.730 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: 7.260 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 30.680 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.016 0.834 10854 Z= 0.907 Angle : 1.440 57.506 14670 Z= 0.822 Chirality : 0.323 6.966 1730 Planarity : 0.008 0.217 1846 Dihedral : 18.831 179.603 4083 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.79 % Favored : 90.99 % Rotamer: Outliers : 0.79 % Allowed : 3.43 % Favored : 95.78 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % 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: -2.29 (0.22), residues: 1354 helix: -0.99 (0.20), residues: 662 sheet: -1.47 (0.44), residues: 124 loop : -2.07 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 66 HIS 0.012 0.002 HIS B 427 PHE 0.025 0.002 PHE A 230 TYR 0.030 0.002 TYR A 393 ARG 0.021 0.001 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 394 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8666 (tttp) cc_final: 0.8404 (tptp) REVERT: A 348 THR cc_start: 0.8411 (m) cc_final: 0.8155 (p) REVERT: A 432 THR cc_start: 0.8355 (p) cc_final: 0.7977 (t) REVERT: A 505 ASP cc_start: 0.7063 (t70) cc_final: 0.6672 (t0) REVERT: A 515 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7895 (p) REVERT: A 542 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8341 (pt) REVERT: B 75 MET cc_start: 0.7818 (mmt) cc_final: 0.7500 (tpp) REVERT: B 519 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8142 (mm) REVERT: B 553 ASP cc_start: 0.7413 (t0) cc_final: 0.7022 (t0) REVERT: C 93 TYR cc_start: 0.7308 (m-80) cc_final: 0.6798 (m-80) outliers start: 9 outliers final: 1 residues processed: 397 average time/residue: 0.2758 time to fit residues: 145.6514 Evaluate side-chains 254 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 250 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 519 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 105 optimal weight: 0.0470 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN B 198 ASN B 202 GLN B 563 ASN C 47 ASN C 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10854 Z= 0.204 Angle : 0.872 24.122 14670 Z= 0.397 Chirality : 0.066 2.046 1730 Planarity : 0.005 0.046 1846 Dihedral : 20.939 171.604 1649 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Rotamer: Outliers : 3.51 % Allowed : 15.20 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1354 helix: -0.40 (0.20), residues: 680 sheet: -0.82 (0.42), residues: 137 loop : -1.51 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.004 0.001 HIS B 568 PHE 0.022 0.002 PHE A 230 TYR 0.017 0.002 TYR A 268 ARG 0.006 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 274 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7234 (tt) REVERT: A 197 GLN cc_start: 0.8180 (mp10) cc_final: 0.7507 (mp10) REVERT: A 296 ARG cc_start: 0.7289 (ttt180) cc_final: 0.6912 (ttt-90) REVERT: A 348 THR cc_start: 0.8482 (m) cc_final: 0.8243 (p) REVERT: A 409 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7862 (mt-10) REVERT: A 432 THR cc_start: 0.8388 (p) cc_final: 0.7967 (t) REVERT: B 124 LEU cc_start: 0.8186 (mt) cc_final: 0.7903 (mt) REVERT: B 127 ARG cc_start: 0.7738 (mtt90) cc_final: 0.7308 (ttm-80) REVERT: B 312 MET cc_start: 0.6390 (tpt) cc_final: 0.6115 (tpt) REVERT: C 38 ARG cc_start: 0.8073 (ttp-110) cc_final: 0.7543 (mtp-110) REVERT: C 80 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8469 (tt) REVERT: C 85 LEU cc_start: 0.8675 (mt) cc_final: 0.7403 (tt) REVERT: C 86 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8374 (pttp) REVERT: C 93 TYR cc_start: 0.7839 (m-80) cc_final: 0.7523 (m-80) outliers start: 40 outliers final: 25 residues processed: 296 average time/residue: 0.2468 time to fit residues: 98.8174 Evaluate side-chains 252 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 225 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 103 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 444 GLN A 562 HIS B 256 GLN B 326 GLN B 563 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10854 Z= 0.255 Angle : 0.798 23.900 14670 Z= 0.370 Chirality : 0.066 2.074 1730 Planarity : 0.005 0.037 1846 Dihedral : 21.328 178.770 1641 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.72 % Favored : 93.21 % Rotamer: Outliers : 4.13 % Allowed : 17.57 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.23), residues: 1354 helix: -0.24 (0.20), residues: 682 sheet: -1.05 (0.39), residues: 160 loop : -1.40 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS B 568 PHE 0.024 0.002 PHE A 230 TYR 0.015 0.002 TYR A 410 ARG 0.005 0.001 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 247 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ARG cc_start: 0.7612 (ttm170) cc_final: 0.7246 (ttm110) REVERT: A 132 SER cc_start: 0.8637 (m) cc_final: 0.8113 (p) REVERT: A 196 MET cc_start: 0.3242 (OUTLIER) cc_final: 0.2447 (tmm) REVERT: A 210 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.6614 (mtm) REVERT: A 348 THR cc_start: 0.8422 (m) cc_final: 0.8066 (p) REVERT: B 124 LEU cc_start: 0.8180 (mt) cc_final: 0.7856 (mt) REVERT: B 200 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7225 (mpp) REVERT: B 210 MET cc_start: 0.7412 (mtm) cc_final: 0.7132 (mtm) REVERT: B 312 MET cc_start: 0.6552 (tpt) cc_final: 0.6310 (tpt) REVERT: B 355 ASP cc_start: 0.7811 (p0) cc_final: 0.7576 (p0) REVERT: B 452 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7970 (tp30) REVERT: B 563 ASN cc_start: 0.6992 (m-40) cc_final: 0.6747 (t0) REVERT: C 38 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7596 (mtp-110) REVERT: C 80 LEU cc_start: 0.8445 (tt) cc_final: 0.8199 (tt) REVERT: C 85 LEU cc_start: 0.8643 (mt) cc_final: 0.7783 (tt) REVERT: C 86 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8565 (pttm) REVERT: D 37 TYR cc_start: 0.8025 (m-80) cc_final: 0.7787 (m-80) REVERT: D 76 SER cc_start: 0.8013 (m) cc_final: 0.7629 (p) REVERT: D 86 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8663 (mmtp) outliers start: 47 outliers final: 34 residues processed: 272 average time/residue: 0.2059 time to fit residues: 78.7552 Evaluate side-chains 258 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 221 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 0.0170 chunk 115 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN B 202 GLN B 256 GLN D 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10854 Z= 0.182 Angle : 0.748 24.347 14670 Z= 0.342 Chirality : 0.064 2.034 1730 Planarity : 0.004 0.033 1846 Dihedral : 21.356 175.747 1641 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.60 % Allowed : 19.86 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.23), residues: 1354 helix: 0.02 (0.20), residues: 684 sheet: -0.74 (0.40), residues: 161 loop : -1.29 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.003 0.001 HIS B 568 PHE 0.036 0.002 PHE B 462 TYR 0.013 0.001 TYR A 130 ARG 0.008 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 250 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ARG cc_start: 0.7692 (ttm170) cc_final: 0.7338 (ttm110) REVERT: A 132 SER cc_start: 0.8517 (m) cc_final: 0.8018 (p) REVERT: A 174 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7355 (tt) REVERT: A 210 MET cc_start: 0.7572 (ttp) cc_final: 0.6622 (mtm) REVERT: A 348 THR cc_start: 0.8462 (m) cc_final: 0.8063 (p) REVERT: B 127 ARG cc_start: 0.7910 (ttt90) cc_final: 0.7540 (ttp-170) REVERT: B 210 MET cc_start: 0.7396 (mtm) cc_final: 0.7048 (ptp) REVERT: B 256 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: B 355 ASP cc_start: 0.7847 (p0) cc_final: 0.7597 (p0) REVERT: B 517 ARG cc_start: 0.8462 (tmm160) cc_final: 0.8216 (ttp80) REVERT: B 563 ASN cc_start: 0.7023 (m-40) cc_final: 0.6762 (t0) REVERT: C 38 ARG cc_start: 0.8304 (ttp-110) cc_final: 0.7659 (mtp-110) REVERT: C 72 ASP cc_start: 0.7913 (m-30) cc_final: 0.7625 (m-30) REVERT: C 85 LEU cc_start: 0.8615 (mt) cc_final: 0.7742 (tt) REVERT: C 86 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8448 (pttm) REVERT: D 76 SER cc_start: 0.8004 (m) cc_final: 0.7688 (p) REVERT: D 85 LEU cc_start: 0.8961 (mt) cc_final: 0.8706 (mp) outliers start: 41 outliers final: 29 residues processed: 272 average time/residue: 0.2041 time to fit residues: 78.0907 Evaluate side-chains 258 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 227 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 527 GLN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 78 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 0.0000 chunk 96 optimal weight: 0.0570 chunk 53 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 0.0170 chunk 116 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN B 198 ASN B 202 GLN B 256 GLN B 424 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10854 Z= 0.183 Angle : 0.746 24.317 14670 Z= 0.340 Chirality : 0.064 2.033 1730 Planarity : 0.004 0.032 1846 Dihedral : 21.472 179.835 1641 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.31 % Allowed : 21.18 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.23), residues: 1354 helix: 0.12 (0.20), residues: 688 sheet: -0.63 (0.40), residues: 161 loop : -1.28 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.003 0.001 HIS B 568 PHE 0.023 0.001 PHE B 580 TYR 0.019 0.001 TYR A 439 ARG 0.005 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 230 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 127 ARG cc_start: 0.7708 (ttm170) cc_final: 0.7310 (ttm110) REVERT: A 174 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7377 (tt) REVERT: A 200 MET cc_start: 0.8179 (mmm) cc_final: 0.7853 (mmm) REVERT: A 210 MET cc_start: 0.7572 (ttp) cc_final: 0.6757 (mtm) REVERT: A 296 ARG cc_start: 0.7330 (ttt180) cc_final: 0.6797 (ttp80) REVERT: A 348 THR cc_start: 0.8466 (m) cc_final: 0.8039 (p) REVERT: A 578 MET cc_start: 0.8203 (mmm) cc_final: 0.7949 (mmt) REVERT: B 210 MET cc_start: 0.7384 (mtm) cc_final: 0.7020 (ptp) REVERT: B 256 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: B 355 ASP cc_start: 0.7852 (p0) cc_final: 0.7566 (p0) REVERT: B 488 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7870 (mtp-110) REVERT: C 38 ARG cc_start: 0.8330 (ttp-110) cc_final: 0.7686 (mtp-110) REVERT: C 72 ASP cc_start: 0.7813 (m-30) cc_final: 0.7384 (m-30) REVERT: C 85 LEU cc_start: 0.8615 (mt) cc_final: 0.7667 (tt) REVERT: C 86 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8452 (pttm) REVERT: D 76 SER cc_start: 0.8118 (m) cc_final: 0.7773 (p) outliers start: 49 outliers final: 39 residues processed: 260 average time/residue: 0.1962 time to fit residues: 73.1894 Evaluate side-chains 265 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 224 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 527 GLN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain D residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.0030 chunk 25 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN D 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10854 Z= 0.175 Angle : 0.742 24.430 14670 Z= 0.338 Chirality : 0.064 2.024 1730 Planarity : 0.004 0.051 1846 Dihedral : 21.491 175.728 1641 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.60 % Allowed : 22.85 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.23), residues: 1354 helix: 0.29 (0.21), residues: 684 sheet: -0.49 (0.40), residues: 159 loop : -1.19 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.003 0.001 HIS B 568 PHE 0.038 0.002 PHE A 115 TYR 0.023 0.001 TYR A 439 ARG 0.004 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 227 time to evaluate : 1.201 Fit side-chains REVERT: A 194 LYS cc_start: 0.9038 (tppt) cc_final: 0.8668 (tppt) REVERT: A 197 GLN cc_start: 0.8158 (mp10) cc_final: 0.7957 (mp10) REVERT: A 200 MET cc_start: 0.8185 (mmm) cc_final: 0.7701 (mpp) REVERT: A 348 THR cc_start: 0.8491 (m) cc_final: 0.8045 (p) REVERT: A 546 ASP cc_start: 0.8171 (t0) cc_final: 0.7677 (t0) REVERT: A 578 MET cc_start: 0.8169 (mmm) cc_final: 0.7966 (mmt) REVERT: B 200 MET cc_start: 0.7350 (mpp) cc_final: 0.6746 (mpp) REVERT: B 210 MET cc_start: 0.7374 (mtm) cc_final: 0.6933 (ptp) REVERT: B 355 ASP cc_start: 0.7819 (p0) cc_final: 0.7522 (p0) REVERT: B 466 MET cc_start: 0.6975 (mtp) cc_final: 0.6695 (mtp) REVERT: B 488 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7928 (mtp-110) REVERT: B 517 ARG cc_start: 0.8561 (tmm160) cc_final: 0.8281 (ttp80) REVERT: C 18 LEU cc_start: 0.8453 (tt) cc_final: 0.8047 (mp) REVERT: C 72 ASP cc_start: 0.7884 (m-30) cc_final: 0.7582 (m-30) REVERT: C 82 MET cc_start: 0.7636 (mpp) cc_final: 0.7128 (mpp) REVERT: C 85 LEU cc_start: 0.8616 (mt) cc_final: 0.7764 (tt) REVERT: C 86 LYS cc_start: 0.8774 (mtmt) cc_final: 0.8307 (pttm) REVERT: D 2 MET cc_start: 0.7899 (tpp) cc_final: 0.7625 (tpp) REVERT: D 76 SER cc_start: 0.8117 (m) cc_final: 0.7772 (p) REVERT: D 82 MET cc_start: 0.7412 (mpp) cc_final: 0.6774 (mpp) outliers start: 41 outliers final: 35 residues processed: 251 average time/residue: 0.1733 time to fit residues: 63.4946 Evaluate side-chains 252 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain D residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10854 Z= 0.198 Angle : 0.754 24.293 14670 Z= 0.341 Chirality : 0.064 2.026 1730 Planarity : 0.004 0.031 1846 Dihedral : 21.435 176.753 1641 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.22 % Allowed : 23.02 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.24), residues: 1354 helix: 0.35 (0.21), residues: 684 sheet: -0.47 (0.41), residues: 161 loop : -1.18 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.002 0.001 HIS A 568 PHE 0.040 0.002 PHE C 29 TYR 0.019 0.001 TYR B 130 ARG 0.005 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 222 time to evaluate : 0.880 Fit side-chains REVERT: A 149 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7664 (mt-10) REVERT: A 194 LYS cc_start: 0.9024 (tppt) cc_final: 0.8679 (tppt) REVERT: A 197 GLN cc_start: 0.8122 (mp10) cc_final: 0.7844 (mp10) REVERT: A 200 MET cc_start: 0.8166 (mmm) cc_final: 0.7787 (mpp) REVERT: A 210 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.6699 (mtp) REVERT: A 348 THR cc_start: 0.8524 (m) cc_final: 0.8076 (p) REVERT: A 578 MET cc_start: 0.8210 (mmm) cc_final: 0.7941 (mmt) REVERT: B 108 MET cc_start: 0.8249 (tpp) cc_final: 0.7926 (tmm) REVERT: B 355 ASP cc_start: 0.7815 (p0) cc_final: 0.7585 (p0) REVERT: B 517 ARG cc_start: 0.8559 (tmm160) cc_final: 0.8310 (ttp80) REVERT: C 18 LEU cc_start: 0.8483 (tt) cc_final: 0.8067 (mp) REVERT: C 82 MET cc_start: 0.7674 (mpp) cc_final: 0.7193 (mpp) REVERT: C 85 LEU cc_start: 0.8582 (mt) cc_final: 0.7746 (tt) REVERT: C 86 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8239 (pttm) REVERT: D 75 LYS cc_start: 0.8525 (tptp) cc_final: 0.8038 (tptp) REVERT: D 76 SER cc_start: 0.8084 (m) cc_final: 0.7743 (p) REVERT: D 82 MET cc_start: 0.7514 (mpp) cc_final: 0.6973 (mpp) outliers start: 48 outliers final: 36 residues processed: 250 average time/residue: 0.1690 time to fit residues: 61.1890 Evaluate side-chains 252 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 215 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 103 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 87 optimal weight: 0.0870 chunk 63 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 101 optimal weight: 0.0870 chunk 117 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: