Starting phenix.real_space_refine on Fri Jul 19 10:39:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6t_37332/07_2024/8w6t_37332.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6t_37332/07_2024/8w6t_37332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6t_37332/07_2024/8w6t_37332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6t_37332/07_2024/8w6t_37332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6t_37332/07_2024/8w6t_37332.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6t_37332/07_2024/8w6t_37332.cif" } resolution = 3.0 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= -0.004 sd= 0.138 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 53 5.16 5 C 5110 2.51 5 N 1158 2.21 5 O 1284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7605 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3857 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 30, 'TRANS': 463} Chain breaks: 3 Chain: "B" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3748 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 30, 'TRANS': 450} Chain breaks: 3 Time building chain proxies: 4.51, per 1000 atoms: 0.59 Number of scatterers: 7605 At special positions: 0 Unit cell: (92.395, 94.569, 107.613, 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 53 16.00 O 1284 8.00 N 1158 7.00 C 5110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 2 sheets defined 71.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.791A pdb=" N LEU A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 22 removed outlier: 4.262A pdb=" N VAL A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 17 " --> pdb=" O PHE A 13 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.719A pdb=" N ILE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.660A pdb=" N TRP A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.528A pdb=" N LEU A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 83 through 102 removed outlier: 3.878A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.530A pdb=" N MET A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 135 removed outlier: 3.646A pdb=" N THR A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 160 removed outlier: 3.797A pdb=" N MET A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Proline residue: A 149 - end of helix removed outlier: 3.691A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 removed outlier: 3.979A pdb=" N LYS A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 259 through 273 removed outlier: 3.824A pdb=" N LEU A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 309 Proline residue: A 290 - end of helix removed outlier: 3.791A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.608A pdb=" N ALA A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 363 removed outlier: 3.681A pdb=" N ILE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.557A pdb=" N ALA A 374 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 377 " --> pdb=" O ALA A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.689A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 removed outlier: 3.706A pdb=" N SER A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 453 removed outlier: 3.958A pdb=" N ALA A 436 " --> pdb=" O PRO A 432 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.522A pdb=" N ILE A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 508 removed outlier: 3.529A pdb=" N ILE A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) Proline residue: A 499 - end of helix Proline residue: A 503 - end of helix removed outlier: 3.919A pdb=" N GLU A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 removed outlier: 3.592A pdb=" N SER A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.526A pdb=" N ILE A 538 " --> pdb=" O PRO A 534 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 534 through 539' Processing helix chain 'A' and resid 540 through 543 removed outlier: 3.846A pdb=" N GLY A 543 " --> pdb=" O PHE A 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 543' Processing helix chain 'A' and resid 546 through 569 removed outlier: 3.523A pdb=" N MET A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'B' and resid 13 through 18 removed outlier: 3.989A pdb=" N VAL B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 50 removed outlier: 3.863A pdb=" N THR B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 61 through 69 removed outlier: 3.803A pdb=" N LEU B 66 " --> pdb=" O PRO B 62 " (cutoff:3.500A) Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 73 through 79 removed outlier: 3.749A pdb=" N SER B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 83 through 102 removed outlier: 4.225A pdb=" N LEU B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 removed outlier: 4.811A pdb=" N MET B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 159 removed outlier: 3.627A pdb=" N ALA B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 149 - end of helix removed outlier: 3.702A pdb=" N ALA B 153 " --> pdb=" O PRO B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 251 removed outlier: 3.539A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 245 " --> pdb=" O CYS B 241 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 removed outlier: 3.574A pdb=" N GLY B 258 " --> pdb=" O THR B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.696A pdb=" N LEU B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.662A pdb=" N THR B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Proline residue: B 290 - end of helix removed outlier: 3.702A pdb=" N ILE B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.735A pdb=" N ILE B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 360 removed outlier: 3.660A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 385 through 394 removed outlier: 3.697A pdb=" N ALA B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 removed outlier: 3.525A pdb=" N SER B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.909A pdb=" N ALA B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 removed outlier: 3.627A pdb=" N TRP B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLY B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 removed outlier: 3.531A pdb=" N SER B 467 " --> pdb=" O PRO B 464 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 468 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.584A pdb=" N ILE B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 removed outlier: 3.747A pdb=" N ILE B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 497 " --> pdb=" O THR B 493 " (cutoff:3.500A) Proline residue: B 499 - end of helix Proline residue: B 503 - end of helix removed outlier: 3.781A pdb=" N ILE B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 522 removed outlier: 3.736A pdb=" N ILE B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 3.505A pdb=" N LEU B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS B 522 " --> pdb=" O PRO B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 546 through 567 removed outlier: 4.037A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 560 " --> pdb=" O GLY B 556 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.483A pdb=" N SER A 419 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 400 through 402 removed outlier: 6.909A pdb=" N SER B 419 " --> pdb=" O ALA B 401 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 990 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: 1.87 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1116 1.27 - 1.41: 1999 1.41 - 1.54: 4533 1.54 - 1.68: 94 1.68 - 1.81: 86 Bond restraints: 7828 Sorted by residual: bond pdb=" C PRO B 535 " pdb=" O PRO B 535 " ideal model delta sigma weight residual 1.235 1.144 0.091 1.30e-02 5.92e+03 4.89e+01 bond pdb=" C LEU B 528 " pdb=" O LEU B 528 " ideal model delta sigma weight residual 1.234 1.157 0.077 1.17e-02 7.31e+03 4.37e+01 bond pdb=" CA ASN B 536 " pdb=" CB ASN B 536 " ideal model delta sigma weight residual 1.530 1.439 0.090 1.64e-02 3.72e+03 3.03e+01 bond pdb=" CA ALA B 537 " pdb=" C ALA B 537 " ideal model delta sigma weight residual 1.526 1.576 -0.050 9.20e-03 1.18e+04 3.00e+01 bond pdb=" CG ASN B 536 " pdb=" OD1 ASN B 536 " ideal model delta sigma weight residual 1.231 1.141 0.090 1.90e-02 2.77e+03 2.27e+01 ... (remaining 7823 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.51: 318 106.51 - 113.44: 4305 113.44 - 120.36: 3136 120.36 - 127.28: 2816 127.28 - 134.20: 134 Bond angle restraints: 10709 Sorted by residual: angle pdb=" N LEU B 528 " pdb=" CA LEU B 528 " pdb=" C LEU B 528 " ideal model delta sigma weight residual 111.96 131.34 -19.38 1.41e+00 5.03e-01 1.89e+02 angle pdb=" CA ALA B 537 " pdb=" C ALA B 537 " pdb=" O ALA B 537 " ideal model delta sigma weight residual 120.71 113.79 6.92 1.10e+00 8.26e-01 3.96e+01 angle pdb=" N LEU B 125 " pdb=" CA LEU B 125 " pdb=" C LEU B 125 " ideal model delta sigma weight residual 113.18 105.91 7.27 1.33e+00 5.65e-01 2.99e+01 angle pdb=" C LEU B 253 " pdb=" N THR B 254 " pdb=" CA THR B 254 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.85e+01 angle pdb=" N TYR B 39 " pdb=" CA TYR B 39 " pdb=" C TYR B 39 " ideal model delta sigma weight residual 113.18 106.51 6.67 1.33e+00 5.65e-01 2.51e+01 ... (remaining 10704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 4039 15.51 - 31.02: 406 31.02 - 46.53: 80 46.53 - 62.04: 6 62.04 - 77.55: 4 Dihedral angle restraints: 4535 sinusoidal: 1697 harmonic: 2838 Sorted by residual: dihedral pdb=" N LEU B 528 " pdb=" C LEU B 528 " pdb=" CA LEU B 528 " pdb=" CB LEU B 528 " ideal model delta harmonic sigma weight residual 122.80 154.03 -31.23 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" C LEU B 528 " pdb=" N LEU B 528 " pdb=" CA LEU B 528 " pdb=" CB LEU B 528 " ideal model delta harmonic sigma weight residual -122.60 -153.26 30.66 0 2.50e+00 1.60e-01 1.50e+02 dihedral pdb=" CA VAL B 20 " pdb=" C VAL B 20 " pdb=" N LEU B 21 " pdb=" CA LEU B 21 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 4532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.275: 1289 0.275 - 0.551: 1 0.551 - 0.826: 0 0.826 - 1.102: 0 1.102 - 1.377: 1 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CA LEU B 528 " pdb=" N LEU B 528 " pdb=" C LEU B 528 " pdb=" CB LEU B 528 " both_signs ideal model delta sigma weight residual False 2.51 1.13 1.38 2.00e-01 2.50e+01 4.74e+01 chirality pdb=" CA PRO B 535 " pdb=" N PRO B 535 " pdb=" C PRO B 535 " pdb=" CB PRO B 535 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ASN B 536 " pdb=" N ASN B 536 " pdb=" C ASN B 536 " pdb=" CB ASN B 536 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1288 not shown) Planarity restraints: 1274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 463 " 0.052 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO B 464 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 464 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 464 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 53 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO B 54 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " -0.048 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A 25 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " -0.040 5.00e-02 4.00e+02 ... (remaining 1271 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1624 2.78 - 3.31: 6750 3.31 - 3.84: 12276 3.84 - 4.37: 14932 4.37 - 4.90: 25544 Nonbonded interactions: 61126 Sorted by model distance: nonbonded pdb=" O PHE B 15 " pdb=" OG1 THR B 19 " model vdw 2.247 2.440 nonbonded pdb=" O PRO B 534 " pdb=" N ALA B 537 " model vdw 2.284 2.520 nonbonded pdb=" O ALA B 59 " pdb=" OH TYR B 81 " model vdw 2.293 2.440 nonbonded pdb=" N ASN B 536 " pdb=" OD1 ASN B 536 " model vdw 2.298 2.520 nonbonded pdb=" O PHE A 42 " pdb=" OG1 THR A 46 " model vdw 2.300 2.440 ... (remaining 61121 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 8 through 161 or resid 233 through 309 or resid 325 throug \ h 403 or resid 418 through 588)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.030 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.006 0.116 7828 Z= 0.360 Angle : 1.028 19.379 10709 Z= 0.589 Chirality : 0.065 1.377 1291 Planarity : 0.009 0.077 1274 Dihedral : 12.770 77.551 2693 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.64 % Rotamer: Outliers : 0.72 % Allowed : 5.74 % Favored : 93.54 % Cbeta Deviations : 0.11 % 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: -5.55 (0.19), residues: 959 helix: -3.67 (0.12), residues: 638 sheet: None (None), residues: 0 loop : -3.26 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 48 HIS 0.005 0.001 HIS A 105 PHE 0.025 0.002 PHE A 287 TYR 0.016 0.001 TYR A 514 ARG 0.003 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 344 ARG cc_start: 0.7225 (ptt180) cc_final: 0.6817 (mmt180) REVERT: A 566 MET cc_start: 0.7882 (mmm) cc_final: 0.7674 (mmm) REVERT: A 576 MET cc_start: 0.7125 (mtp) cc_final: 0.6855 (ttm) REVERT: B 456 LYS cc_start: 0.7222 (ttmt) cc_final: 0.6990 (ttmm) REVERT: B 533 ASN cc_start: 0.6190 (t0) cc_final: 0.5500 (m110) REVERT: B 566 MET cc_start: 0.6575 (mmm) cc_final: 0.5731 (mmt) outliers start: 6 outliers final: 3 residues processed: 158 average time/residue: 1.0072 time to fit residues: 169.7195 Evaluate side-chains 105 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 536 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS A 338 GLN B 86 HIS B 157 GLN B 234 HIS B 460 ASN B 490 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7828 Z= 0.210 Angle : 0.653 6.926 10709 Z= 0.332 Chirality : 0.041 0.159 1291 Planarity : 0.007 0.055 1274 Dihedral : 5.802 35.989 1018 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.87 % Allowed : 14.11 % Favored : 83.01 % 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: -3.36 (0.25), residues: 959 helix: -1.89 (0.18), residues: 655 sheet: None (None), residues: 0 loop : -2.64 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 48 HIS 0.004 0.001 HIS A 105 PHE 0.013 0.001 PHE B 15 TYR 0.009 0.001 TYR B 514 ARG 0.002 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 267 GLU cc_start: 0.7517 (pp20) cc_final: 0.7204 (pt0) REVERT: A 329 CYS cc_start: 0.7507 (m) cc_final: 0.7157 (t) REVERT: A 344 ARG cc_start: 0.7295 (ptt180) cc_final: 0.6912 (mmt180) REVERT: A 460 ASN cc_start: 0.7415 (m-40) cc_final: 0.6854 (t0) REVERT: A 566 MET cc_start: 0.7941 (mmm) cc_final: 0.7738 (mmm) REVERT: B 450 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: B 566 MET cc_start: 0.6359 (mmm) cc_final: 0.5382 (mmt) outliers start: 24 outliers final: 13 residues processed: 132 average time/residue: 0.8857 time to fit residues: 125.9469 Evaluate side-chains 111 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7828 Z= 0.175 Angle : 0.592 6.110 10709 Z= 0.300 Chirality : 0.040 0.141 1291 Planarity : 0.005 0.053 1274 Dihedral : 5.201 25.684 1014 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.35 % Allowed : 16.99 % Favored : 79.67 % 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: -2.33 (0.27), residues: 959 helix: -0.99 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.59 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 48 HIS 0.004 0.001 HIS A 105 PHE 0.013 0.001 PHE B 354 TYR 0.009 0.001 TYR B 580 ARG 0.001 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 329 CYS cc_start: 0.7429 (m) cc_final: 0.7077 (t) REVERT: A 344 ARG cc_start: 0.7424 (ptt180) cc_final: 0.6996 (mmt180) REVERT: A 460 ASN cc_start: 0.7325 (m-40) cc_final: 0.6824 (t0) REVERT: A 566 MET cc_start: 0.7942 (mmm) cc_final: 0.7673 (mmm) REVERT: B 450 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: B 555 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7175 (pt) REVERT: B 566 MET cc_start: 0.6335 (mmm) cc_final: 0.5344 (mmp) outliers start: 28 outliers final: 14 residues processed: 129 average time/residue: 0.9155 time to fit residues: 126.8676 Evaluate side-chains 119 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 0.0270 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7828 Z= 0.309 Angle : 0.694 7.885 10709 Z= 0.351 Chirality : 0.044 0.154 1291 Planarity : 0.006 0.057 1274 Dihedral : 5.475 27.117 1012 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.67 % Allowed : 16.75 % Favored : 78.59 % 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: -2.07 (0.27), residues: 959 helix: -0.80 (0.20), residues: 669 sheet: None (None), residues: 0 loop : -2.53 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 48 HIS 0.006 0.001 HIS A 105 PHE 0.023 0.002 PHE B 15 TYR 0.013 0.002 TYR B 514 ARG 0.002 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 105 time to evaluate : 0.840 Fit side-chains REVERT: A 68 MET cc_start: 0.8234 (mtp) cc_final: 0.8021 (mmm) REVERT: A 148 MET cc_start: 0.8483 (tpt) cc_final: 0.7765 (tpt) REVERT: A 329 CYS cc_start: 0.7483 (m) cc_final: 0.7201 (m) REVERT: A 344 ARG cc_start: 0.7494 (ptt180) cc_final: 0.7064 (mmt180) REVERT: A 460 ASN cc_start: 0.7620 (m-40) cc_final: 0.6952 (t0) REVERT: A 566 MET cc_start: 0.7958 (mmm) cc_final: 0.7753 (mmm) REVERT: B 450 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: B 555 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7228 (pt) REVERT: B 566 MET cc_start: 0.6521 (mmm) cc_final: 0.5412 (mmt) REVERT: B 576 MET cc_start: 0.6807 (ttt) cc_final: 0.6592 (ttm) outliers start: 39 outliers final: 23 residues processed: 131 average time/residue: 0.8536 time to fit residues: 120.9239 Evaluate side-chains 124 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.6980 chunk 53 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7828 Z= 0.158 Angle : 0.588 7.266 10709 Z= 0.293 Chirality : 0.039 0.139 1291 Planarity : 0.005 0.051 1274 Dihedral : 4.997 25.134 1012 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.99 % Allowed : 19.62 % Favored : 77.39 % 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: -1.47 (0.28), residues: 959 helix: -0.29 (0.21), residues: 665 sheet: None (None), residues: 0 loop : -2.43 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 48 HIS 0.003 0.001 HIS A 105 PHE 0.015 0.001 PHE B 354 TYR 0.007 0.001 TYR B 337 ARG 0.002 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 0.875 Fit side-chains REVERT: A 68 MET cc_start: 0.8165 (mtp) cc_final: 0.7949 (mmm) REVERT: A 148 MET cc_start: 0.8435 (tpt) cc_final: 0.7713 (tpt) REVERT: A 329 CYS cc_start: 0.7411 (m) cc_final: 0.6900 (m) REVERT: A 344 ARG cc_start: 0.7454 (ptt180) cc_final: 0.6971 (mmt180) REVERT: A 460 ASN cc_start: 0.7407 (m-40) cc_final: 0.6912 (t0) REVERT: A 566 MET cc_start: 0.7949 (mmm) cc_final: 0.7686 (mmm) REVERT: B 385 ASP cc_start: 0.8322 (m-30) cc_final: 0.8030 (m-30) REVERT: B 450 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6753 (tm-30) REVERT: B 555 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7236 (pt) REVERT: B 566 MET cc_start: 0.6415 (mmm) cc_final: 0.5421 (mmp) REVERT: B 576 MET cc_start: 0.6750 (ttt) cc_final: 0.6545 (ttm) outliers start: 25 outliers final: 14 residues processed: 117 average time/residue: 0.9599 time to fit residues: 120.8490 Evaluate side-chains 114 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.0070 chunk 7 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 chunk 90 optimal weight: 0.0970 overall best weight: 0.0710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 105 HIS B 533 ASN B 544 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7828 Z= 0.138 Angle : 0.552 6.030 10709 Z= 0.275 Chirality : 0.038 0.135 1291 Planarity : 0.005 0.048 1274 Dihedral : 4.493 23.958 1012 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.03 % Allowed : 20.93 % Favored : 77.03 % 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: -0.85 (0.28), residues: 959 helix: 0.23 (0.21), residues: 654 sheet: None (None), residues: 0 loop : -2.24 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 372 HIS 0.002 0.000 HIS A 105 PHE 0.019 0.001 PHE B 354 TYR 0.007 0.001 TYR A 39 ARG 0.004 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.889 Fit side-chains REVERT: A 344 ARG cc_start: 0.7506 (ptt180) cc_final: 0.6950 (mmt180) REVERT: A 460 ASN cc_start: 0.7321 (m-40) cc_final: 0.6959 (t0) REVERT: A 566 MET cc_start: 0.8002 (mmm) cc_final: 0.7726 (mmm) REVERT: B 57 VAL cc_start: 0.8391 (t) cc_final: 0.8106 (t) REVERT: B 385 ASP cc_start: 0.8174 (m-30) cc_final: 0.7865 (m-30) REVERT: B 450 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: B 555 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7183 (pt) REVERT: B 566 MET cc_start: 0.6354 (mmm) cc_final: 0.5500 (mmp) outliers start: 17 outliers final: 6 residues processed: 130 average time/residue: 0.8659 time to fit residues: 121.5790 Evaluate side-chains 119 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 58 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 43 optimal weight: 0.0020 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 460 ASN B 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7828 Z= 0.154 Angle : 0.585 11.556 10709 Z= 0.289 Chirality : 0.039 0.133 1291 Planarity : 0.005 0.049 1274 Dihedral : 4.470 24.598 1012 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.91 % Allowed : 22.13 % Favored : 75.96 % 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 (0.28), residues: 959 helix: 0.44 (0.21), residues: 656 sheet: None (None), residues: 0 loop : -2.22 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 48 HIS 0.002 0.001 HIS A 105 PHE 0.022 0.001 PHE B 354 TYR 0.010 0.001 TYR A 542 ARG 0.005 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.830 Fit side-chains REVERT: A 344 ARG cc_start: 0.7514 (ptt180) cc_final: 0.6956 (mmt180) REVERT: A 566 MET cc_start: 0.7954 (mmm) cc_final: 0.7719 (mmm) REVERT: B 57 VAL cc_start: 0.8580 (t) cc_final: 0.8329 (t) REVERT: B 450 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: B 555 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7261 (pt) REVERT: B 566 MET cc_start: 0.6379 (mmm) cc_final: 0.5400 (mmp) outliers start: 16 outliers final: 7 residues processed: 124 average time/residue: 0.9009 time to fit residues: 120.5837 Evaluate side-chains 116 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 156 GLN B 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7828 Z= 0.238 Angle : 0.642 8.099 10709 Z= 0.321 Chirality : 0.042 0.135 1291 Planarity : 0.005 0.051 1274 Dihedral : 4.880 26.039 1012 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.75 % Allowed : 21.65 % Favored : 75.60 % 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: -0.77 (0.28), residues: 959 helix: 0.27 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -2.24 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 48 HIS 0.004 0.001 HIS A 105 PHE 0.021 0.001 PHE B 354 TYR 0.014 0.002 TYR A 514 ARG 0.002 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.805 Fit side-chains REVERT: A 329 CYS cc_start: 0.7470 (m) cc_final: 0.6992 (m) REVERT: A 338 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: A 344 ARG cc_start: 0.7559 (ptt180) cc_final: 0.6993 (mmt180) REVERT: A 357 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8709 (ttp) REVERT: A 460 ASN cc_start: 0.7475 (m-40) cc_final: 0.6966 (t0) REVERT: A 566 MET cc_start: 0.8012 (mmm) cc_final: 0.7765 (mmm) REVERT: B 256 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7956 (mp) REVERT: B 450 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6806 (tm-30) REVERT: B 555 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7183 (pt) REVERT: B 566 MET cc_start: 0.6380 (mmm) cc_final: 0.5339 (mmp) outliers start: 23 outliers final: 14 residues processed: 120 average time/residue: 0.8783 time to fit residues: 113.8114 Evaluate side-chains 119 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7828 Z= 0.181 Angle : 0.607 8.699 10709 Z= 0.304 Chirality : 0.040 0.149 1291 Planarity : 0.005 0.050 1274 Dihedral : 4.723 24.232 1012 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.39 % Allowed : 22.13 % Favored : 75.48 % 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: -0.64 (0.28), residues: 959 helix: 0.41 (0.21), residues: 663 sheet: None (None), residues: 0 loop : -2.29 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 48 HIS 0.004 0.001 HIS A 105 PHE 0.019 0.001 PHE B 354 TYR 0.008 0.001 TYR A 514 ARG 0.002 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.823 Fit side-chains REVERT: A 148 MET cc_start: 0.8429 (tpt) cc_final: 0.7693 (tpt) REVERT: A 329 CYS cc_start: 0.7463 (m) cc_final: 0.7012 (m) REVERT: A 338 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: A 344 ARG cc_start: 0.7567 (ptt180) cc_final: 0.7005 (mmt180) REVERT: A 357 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8684 (ttp) REVERT: A 460 ASN cc_start: 0.7432 (m-40) cc_final: 0.6988 (t0) REVERT: B 256 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7800 (mp) REVERT: B 285 PHE cc_start: 0.6511 (t80) cc_final: 0.6246 (t80) REVERT: B 385 ASP cc_start: 0.8334 (m-30) cc_final: 0.8021 (m-30) REVERT: B 450 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6720 (tm-30) REVERT: B 555 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7151 (pt) REVERT: B 566 MET cc_start: 0.6411 (mmm) cc_final: 0.5387 (mmp) outliers start: 20 outliers final: 13 residues processed: 118 average time/residue: 0.9060 time to fit residues: 115.0996 Evaluate side-chains 121 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7828 Z= 0.180 Angle : 0.606 9.640 10709 Z= 0.303 Chirality : 0.040 0.149 1291 Planarity : 0.005 0.050 1274 Dihedral : 4.660 24.390 1012 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.27 % Allowed : 22.25 % Favored : 75.48 % 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: -0.57 (0.28), residues: 959 helix: 0.47 (0.21), residues: 667 sheet: None (None), residues: 0 loop : -2.35 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 48 HIS 0.004 0.001 HIS A 105 PHE 0.022 0.001 PHE B 354 TYR 0.010 0.001 TYR B 542 ARG 0.003 0.000 ARG B 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.784 Fit side-chains REVERT: A 329 CYS cc_start: 0.7445 (m) cc_final: 0.6980 (m) REVERT: A 338 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: A 344 ARG cc_start: 0.7536 (ptt180) cc_final: 0.6927 (mmt180) REVERT: A 357 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8687 (ttp) REVERT: A 460 ASN cc_start: 0.7371 (m-40) cc_final: 0.6988 (t0) REVERT: B 285 PHE cc_start: 0.6588 (t80) cc_final: 0.6332 (t80) REVERT: B 450 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6661 (tm-30) REVERT: B 552 LYS cc_start: 0.6834 (tppt) cc_final: 0.5659 (ttmm) REVERT: B 555 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7106 (pt) REVERT: B 566 MET cc_start: 0.6377 (mmm) cc_final: 0.5363 (mmp) outliers start: 19 outliers final: 13 residues processed: 120 average time/residue: 0.8754 time to fit residues: 113.3771 Evaluate side-chains 120 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 0.0370 chunk 32 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 4 optimal weight: 0.0870 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.165275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141346 restraints weight = 8966.577| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.35 r_work: 0.3458 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7828 Z= 0.148 Angle : 0.580 11.033 10709 Z= 0.286 Chirality : 0.039 0.148 1291 Planarity : 0.005 0.050 1274 Dihedral : 4.412 23.491 1012 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.03 % Allowed : 22.61 % Favored : 75.36 % 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: -0.32 (0.29), residues: 959 helix: 0.69 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.25 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 372 HIS 0.002 0.000 HIS A 105 PHE 0.024 0.001 PHE B 368 TYR 0.009 0.001 TYR B 10 ARG 0.003 0.000 ARG B 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2783.60 seconds wall clock time: 49 minutes 34.06 seconds (2974.06 seconds total)