Starting phenix.real_space_refine on Sat Aug 3 06:36:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6h_37323/08_2024/8w6h_37323.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6h_37323/08_2024/8w6h_37323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6h_37323/08_2024/8w6h_37323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6h_37323/08_2024/8w6h_37323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6h_37323/08_2024/8w6h_37323.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6h_37323/08_2024/8w6h_37323.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.119 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 Na 2 4.78 5 C 4897 2.51 5 N 1098 2.21 5 O 1219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 11": "NH1" <-> "NH2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "B ARG 11": "NH1" <-> "NH2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B GLU 451": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7268 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3601 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 28, 'TRANS': 433} Chain breaks: 4 Chain: "B" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3599 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 27, 'TRANS': 433} Chain breaks: 4 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' NA': 1, 'CLR': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' NA': 1, 'CLR': 1, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.35, per 1000 atoms: 0.60 Number of scatterers: 7268 At special positions: 0 Unit cell: (96.743, 84.786, 79.351, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 Na 2 11.00 O 1219 8.00 N 1098 7.00 C 4897 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: 2.88 Conformation dependent library (CDL) restraints added in 1.3 seconds 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 73.1% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 removed outlier: 3.979A pdb=" N LEU A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.519A pdb=" N CYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 60 Processing helix chain 'A' and resid 61 through 70 Proline residue: A 67 - end of helix Processing helix chain 'A' and resid 83 through 102 removed outlier: 3.555A pdb=" N GLY A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.785A pdb=" N VAL A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 removed outlier: 3.817A pdb=" N LEU A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 160 removed outlier: 4.042A pdb=" N MET A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.734A pdb=" N THR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.593A pdb=" N PHE A 265 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 308 removed outlier: 3.517A pdb=" N PHE A 285 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.890A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.649A pdb=" N LYS A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 364 removed outlier: 3.989A pdb=" N ILE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.869A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 removed outlier: 3.503A pdb=" N SER A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.863A pdb=" N ILE A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 removed outlier: 3.746A pdb=" N LYS A 461 " --> pdb=" O TRP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.548A pdb=" N GLY A 466 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 467 " --> pdb=" O PRO A 464 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 468 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.542A pdb=" N ILE A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A 480 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 508 removed outlier: 3.664A pdb=" N PHE A 497 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 498 " --> pdb=" O ILE A 494 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.524A pdb=" N SER A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Proline residue: A 503 - end of helix removed outlier: 3.600A pdb=" N GLU A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 521 Proline residue: A 518 - end of helix Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.554A pdb=" N ILE A 538 " --> pdb=" O PRO A 534 " (cutoff:3.500A) removed outlier: 3.687A 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 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 547 through 572 removed outlier: 3.539A pdb=" N VAL A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.979A pdb=" N LEU B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 50 removed outlier: 3.518A pdb=" N CYS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 46 " --> pdb=" O PHE B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 61 through 70 Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 83 through 102 removed outlier: 3.554A pdb=" N GLY B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 98 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.785A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 removed outlier: 3.816A pdb=" N LEU B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 160 removed outlier: 4.042A pdb=" N MET B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 236 through 251 removed outlier: 3.733A pdb=" N THR B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.593A pdb=" N PHE B 265 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 266 " --> pdb=" O ASN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 308 removed outlier: 3.518A pdb=" N PHE B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Proline residue: B 290 - end of helix removed outlier: 3.890A pdb=" N ILE B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.650A pdb=" N LYS B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 364 removed outlier: 3.988A pdb=" N ILE B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.869A pdb=" N VAL B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 removed outlier: 3.502A pdb=" N SER B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 452 removed outlier: 3.862A pdb=" N ILE B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 452 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 461 removed outlier: 3.746A pdb=" N LYS B 461 " --> pdb=" O TRP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.549A pdb=" N GLY B 466 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 467 " --> pdb=" O PRO B 464 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 468 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.542A pdb=" N ILE B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B 480 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 removed outlier: 3.665A pdb=" N PHE B 497 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 498 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Proline residue: B 499 - end of helix removed outlier: 3.524A pdb=" N SER B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Proline residue: B 503 - end of helix removed outlier: 3.601A pdb=" N GLU B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 521 Proline residue: B 518 - end of helix Processing helix chain 'B' and resid 534 through 539 removed outlier: 3.554A pdb=" N ILE B 538 " --> pdb=" O PRO B 534 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 534 through 539' Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 546 through 572 removed outlier: 3.921A pdb=" N MET B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS B 570 " --> pdb=" O MET B 566 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.792A 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: 6.793A pdb=" N SER B 419 " --> pdb=" O ALA B 401 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 978 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: 1.83 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1049 1.29 - 1.42: 1957 1.42 - 1.55: 4385 1.55 - 1.68: 2 1.68 - 1.81: 82 Bond restraints: 7475 Sorted by residual: bond pdb=" C16 CLR B 603 " pdb=" C17 CLR B 603 " ideal model delta sigma weight residual 1.554 1.442 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C16 CLR A 603 " pdb=" C17 CLR A 603 " ideal model delta sigma weight residual 1.554 1.442 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C13 CLR B 603 " pdb=" C14 CLR B 603 " ideal model delta sigma weight residual 1.537 1.426 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C13 CLR A 603 " pdb=" C14 CLR A 603 " ideal model delta sigma weight residual 1.537 1.427 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C THR B 259 " pdb=" O THR B 259 " ideal model delta sigma weight residual 1.233 1.162 0.071 1.30e-02 5.92e+03 2.95e+01 ... (remaining 7470 not shown) Histogram of bond angle deviations from ideal: 95.44 - 103.17: 137 103.17 - 110.90: 2889 110.90 - 118.63: 3068 118.63 - 126.36: 3947 126.36 - 134.09: 194 Bond angle restraints: 10235 Sorted by residual: angle pdb=" C THR A 259 " pdb=" CA THR A 259 " pdb=" CB THR A 259 " ideal model delta sigma weight residual 110.45 118.40 -7.95 1.73e+00 3.34e-01 2.11e+01 angle pdb=" C THR B 259 " pdb=" CA THR B 259 " pdb=" CB THR B 259 " ideal model delta sigma weight residual 110.45 118.08 -7.63 1.73e+00 3.34e-01 1.95e+01 angle pdb=" C16 CLR B 603 " pdb=" C17 CLR B 603 " pdb=" C20 CLR B 603 " ideal model delta sigma weight residual 112.02 98.98 13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" C16 CLR A 603 " pdb=" C17 CLR A 603 " pdb=" C20 CLR A 603 " ideal model delta sigma weight residual 112.02 99.01 13.01 3.00e+00 1.11e-01 1.88e+01 angle pdb=" N ASN B 119 " pdb=" CA ASN B 119 " pdb=" C ASN B 119 " ideal model delta sigma weight residual 111.53 120.92 -9.39 2.18e+00 2.10e-01 1.86e+01 ... (remaining 10230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 3874 15.99 - 31.99: 454 31.99 - 47.98: 82 47.98 - 63.97: 2 63.97 - 79.96: 10 Dihedral angle restraints: 4422 sinusoidal: 1735 harmonic: 2687 Sorted by residual: dihedral pdb=" CA ASN A 119 " pdb=" C ASN A 119 " pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta harmonic sigma weight residual 180.00 139.58 40.42 0 5.00e+00 4.00e-02 6.53e+01 dihedral pdb=" CA ASN B 119 " pdb=" C ASN B 119 " pdb=" N PRO B 120 " pdb=" CA PRO B 120 " ideal model delta harmonic sigma weight residual 180.00 139.58 40.42 0 5.00e+00 4.00e-02 6.53e+01 dihedral pdb=" CA PRO B 27 " pdb=" C PRO B 27 " pdb=" N ILE B 28 " pdb=" CA ILE B 28 " ideal model delta harmonic sigma weight residual 180.00 149.61 30.39 0 5.00e+00 4.00e-02 3.69e+01 ... (remaining 4419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1109 0.094 - 0.189: 125 0.189 - 0.283: 8 0.283 - 0.377: 6 0.377 - 0.471: 4 Chirality restraints: 1252 Sorted by residual: chirality pdb=" C10 CLR A 603 " pdb=" C1 CLR A 603 " pdb=" C5 CLR A 603 " pdb=" C9 CLR A 603 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" C10 CLR B 603 " pdb=" C1 CLR B 603 " pdb=" C5 CLR B 603 " pdb=" C9 CLR B 603 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1249 not shown) Planarity restraints: 1195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 534 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO B 535 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO B 535 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 535 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 534 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO A 535 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " -0.050 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 27 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.044 5.00e-02 4.00e+02 ... (remaining 1192 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1122 2.74 - 3.28: 6646 3.28 - 3.82: 11202 3.82 - 4.36: 14235 4.36 - 4.90: 24319 Nonbonded interactions: 57524 Sorted by model distance: nonbonded pdb=" O CYS A 243 " pdb=" OG SER A 247 " model vdw 2.205 3.040 nonbonded pdb=" O CYS B 243 " pdb=" OG SER B 247 " model vdw 2.205 3.040 nonbonded pdb=" O TRP A 284 " pdb=" OG SER A 288 " model vdw 2.228 3.040 nonbonded pdb=" O TRP B 284 " pdb=" OG SER B 288 " model vdw 2.228 3.040 nonbonded pdb=" O PHE B 42 " pdb=" OG1 THR B 46 " model vdw 2.274 3.040 ... (remaining 57519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 308 or resid 333 through 364 or resid 381 throug \ h 588 or resid 601 through 603)) selection = (chain 'B' and (resid 9 through 161 or resid 233 through 588 or resid 601 throug \ h 603)) } 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.010 Find NCS groups from input model: 0.310 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.011 0.112 7475 Z= 0.689 Angle : 1.230 13.037 10235 Z= 0.617 Chirality : 0.070 0.471 1252 Planarity : 0.011 0.110 1195 Dihedral : 13.789 79.965 2674 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.52 % Favored : 90.25 % Rotamer: Outliers : 0.76 % Allowed : 9.19 % Favored : 90.05 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.23 % 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: -7.00 (0.15), residues: 903 helix: -4.58 (0.08), residues: 668 sheet: None (None), residues: 0 loop : -3.89 (0.32), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 572 HIS 0.011 0.003 HIS B 105 PHE 0.028 0.002 PHE A 354 TYR 0.011 0.002 TYR A 81 ARG 0.003 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.902 Fit side-chains REVERT: A 65 MET cc_start: 0.8834 (mtp) cc_final: 0.8578 (mtp) REVERT: A 344 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7576 (mtp85) REVERT: B 65 MET cc_start: 0.8735 (mtp) cc_final: 0.8460 (mtp) REVERT: B 68 MET cc_start: 0.7694 (mtm) cc_final: 0.7453 (mtm) REVERT: B 344 ARG cc_start: 0.7816 (mtp180) cc_final: 0.7570 (mtp85) outliers start: 6 outliers final: 0 residues processed: 139 average time/residue: 0.1837 time to fit residues: 34.3864 Evaluate side-chains 111 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 304 GLN B 160 ASN B 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7475 Z= 0.219 Angle : 0.753 11.458 10235 Z= 0.378 Chirality : 0.045 0.241 1252 Planarity : 0.008 0.085 1195 Dihedral : 6.859 57.713 1085 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.39 % Allowed : 11.08 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -3.69 (0.24), residues: 903 helix: -2.22 (0.17), residues: 625 sheet: None (None), residues: 0 loop : -2.57 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 PHE 0.013 0.001 PHE A 287 TYR 0.012 0.002 TYR A 81 ARG 0.007 0.001 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.801 Fit side-chains REVERT: A 157 GLN cc_start: 0.8037 (mt0) cc_final: 0.7688 (mt0) outliers start: 19 outliers final: 12 residues processed: 131 average time/residue: 0.1674 time to fit residues: 30.7225 Evaluate side-chains 125 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7475 Z= 0.219 Angle : 0.677 10.059 10235 Z= 0.337 Chirality : 0.044 0.237 1252 Planarity : 0.006 0.076 1195 Dihedral : 6.159 56.586 1085 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.90 % Allowed : 13.35 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.28), residues: 903 helix: -1.01 (0.21), residues: 645 sheet: None (None), residues: 0 loop : -2.44 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 572 HIS 0.009 0.001 HIS A 105 PHE 0.015 0.001 PHE A 287 TYR 0.023 0.002 TYR A 514 ARG 0.011 0.001 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 0.785 Fit side-chains REVERT: A 71 ILE cc_start: 0.8521 (mm) cc_final: 0.8260 (mt) REVERT: A 157 GLN cc_start: 0.8170 (mt0) cc_final: 0.7876 (mt0) REVERT: A 267 GLU cc_start: 0.7679 (tp30) cc_final: 0.7366 (mm-30) REVERT: B 34 GLU cc_start: 0.7108 (pm20) cc_final: 0.6730 (mp0) REVERT: B 267 GLU cc_start: 0.7658 (tp30) cc_final: 0.7351 (mm-30) outliers start: 23 outliers final: 11 residues processed: 134 average time/residue: 0.1537 time to fit residues: 29.4578 Evaluate side-chains 123 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7475 Z= 0.222 Angle : 0.657 9.143 10235 Z= 0.326 Chirality : 0.044 0.234 1252 Planarity : 0.006 0.072 1195 Dihedral : 5.668 46.233 1085 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.02 % Allowed : 15.11 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.53 (0.29), residues: 903 helix: -0.46 (0.22), residues: 649 sheet: None (None), residues: 0 loop : -2.23 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 572 HIS 0.008 0.001 HIS A 105 PHE 0.015 0.001 PHE B 287 TYR 0.023 0.002 TYR B 514 ARG 0.006 0.001 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.721 Fit side-chains REVERT: A 34 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: A 157 GLN cc_start: 0.8070 (mt0) cc_final: 0.7852 (mt0) REVERT: A 267 GLU cc_start: 0.7616 (tp30) cc_final: 0.7306 (mm-30) REVERT: A 294 ILE cc_start: 0.9003 (mt) cc_final: 0.8734 (mt) REVERT: B 34 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: B 267 GLU cc_start: 0.7624 (tp30) cc_final: 0.7342 (mm-30) REVERT: B 484 LEU cc_start: 0.8996 (tp) cc_final: 0.8709 (tt) outliers start: 24 outliers final: 20 residues processed: 126 average time/residue: 0.1538 time to fit residues: 27.6260 Evaluate side-chains 133 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 0.0000 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 79 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7475 Z= 0.192 Angle : 0.630 8.674 10235 Z= 0.312 Chirality : 0.043 0.232 1252 Planarity : 0.005 0.069 1195 Dihedral : 5.297 36.554 1085 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.65 % Allowed : 15.24 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.10 (0.30), residues: 903 helix: -0.12 (0.22), residues: 653 sheet: None (None), residues: 0 loop : -2.16 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 PHE 0.013 0.001 PHE B 287 TYR 0.023 0.001 TYR A 514 ARG 0.003 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 0.818 Fit side-chains REVERT: A 34 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: A 267 GLU cc_start: 0.7572 (tp30) cc_final: 0.7277 (mm-30) REVERT: A 294 ILE cc_start: 0.9023 (mt) cc_final: 0.8763 (mt) REVERT: B 34 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: B 267 GLU cc_start: 0.7562 (tp30) cc_final: 0.7274 (mm-30) REVERT: B 294 ILE cc_start: 0.9043 (mt) cc_final: 0.8780 (mt) REVERT: B 484 LEU cc_start: 0.9018 (tp) cc_final: 0.8711 (tt) outliers start: 29 outliers final: 19 residues processed: 135 average time/residue: 0.1591 time to fit residues: 30.6201 Evaluate side-chains 134 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 0.049 7475 Z= 0.212 Angle : 0.662 14.290 10235 Z= 0.319 Chirality : 0.044 0.229 1252 Planarity : 0.005 0.067 1195 Dihedral : 5.135 31.442 1085 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.40 % Allowed : 16.50 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.82 (0.30), residues: 903 helix: 0.06 (0.22), residues: 657 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.008 0.001 HIS B 105 PHE 0.014 0.001 PHE B 287 TYR 0.013 0.001 TYR A 39 ARG 0.001 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 0.809 Fit side-chains REVERT: A 34 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: A 243 CYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7782 (p) REVERT: A 267 GLU cc_start: 0.7583 (tp30) cc_final: 0.7378 (mm-30) REVERT: A 294 ILE cc_start: 0.9030 (mt) cc_final: 0.8782 (mt) REVERT: A 484 LEU cc_start: 0.9008 (tp) cc_final: 0.8704 (tt) REVERT: B 34 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: B 267 GLU cc_start: 0.7555 (tp30) cc_final: 0.7265 (mm-30) REVERT: B 294 ILE cc_start: 0.9045 (mt) cc_final: 0.8797 (mt) REVERT: B 484 LEU cc_start: 0.8997 (tp) cc_final: 0.8699 (tt) outliers start: 27 outliers final: 21 residues processed: 132 average time/residue: 0.1548 time to fit residues: 29.1124 Evaluate side-chains 138 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 74 optimal weight: 0.0000 chunk 49 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.0370 overall best weight: 0.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7475 Z= 0.173 Angle : 0.633 12.197 10235 Z= 0.305 Chirality : 0.042 0.227 1252 Planarity : 0.005 0.063 1195 Dihedral : 4.920 30.608 1085 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.77 % Allowed : 16.37 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.58 (0.30), residues: 903 helix: 0.29 (0.23), residues: 647 sheet: None (None), residues: 0 loop : -2.01 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 572 HIS 0.006 0.001 HIS B 105 PHE 0.012 0.001 PHE A 287 TYR 0.011 0.001 TYR A 39 ARG 0.002 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.815 Fit side-chains REVERT: A 34 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: A 243 CYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7968 (p) REVERT: A 267 GLU cc_start: 0.7629 (tp30) cc_final: 0.7427 (mm-30) REVERT: A 270 ASN cc_start: 0.7580 (m-40) cc_final: 0.7203 (m-40) REVERT: A 294 ILE cc_start: 0.9005 (mt) cc_final: 0.8762 (mt) REVERT: A 484 LEU cc_start: 0.8975 (tp) cc_final: 0.8671 (tt) REVERT: B 34 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: B 294 ILE cc_start: 0.9014 (mt) cc_final: 0.8782 (mt) REVERT: B 484 LEU cc_start: 0.9020 (tp) cc_final: 0.8708 (tt) outliers start: 22 outliers final: 16 residues processed: 138 average time/residue: 0.1520 time to fit residues: 30.0370 Evaluate side-chains 140 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 460 ASN B 460 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7475 Z= 0.204 Angle : 0.649 11.786 10235 Z= 0.311 Chirality : 0.043 0.227 1252 Planarity : 0.005 0.065 1195 Dihedral : 4.927 30.570 1085 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.90 % Allowed : 16.50 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.52 (0.30), residues: 903 helix: 0.35 (0.23), residues: 651 sheet: None (None), residues: 0 loop : -2.04 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 PHE 0.013 0.001 PHE A 287 TYR 0.022 0.001 TYR B 514 ARG 0.003 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.893 Fit side-chains REVERT: A 34 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: A 267 GLU cc_start: 0.7671 (tp30) cc_final: 0.7469 (mm-30) REVERT: A 294 ILE cc_start: 0.9024 (mt) cc_final: 0.8783 (mt) REVERT: A 484 LEU cc_start: 0.9023 (tp) cc_final: 0.8706 (tt) REVERT: B 294 ILE cc_start: 0.9023 (mt) cc_final: 0.8811 (mt) REVERT: B 484 LEU cc_start: 0.9030 (tp) cc_final: 0.8726 (tt) outliers start: 23 outliers final: 19 residues processed: 135 average time/residue: 0.1577 time to fit residues: 30.6799 Evaluate side-chains 141 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7475 Z= 0.186 Angle : 0.636 11.264 10235 Z= 0.306 Chirality : 0.042 0.225 1252 Planarity : 0.005 0.064 1195 Dihedral : 4.881 30.045 1085 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.64 % Allowed : 17.00 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -0.44 (0.30), residues: 903 helix: 0.43 (0.23), residues: 643 sheet: None (None), residues: 0 loop : -2.04 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 PHE 0.013 0.001 PHE A 287 TYR 0.010 0.001 TYR A 39 ARG 0.001 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 0.924 Fit side-chains REVERT: A 34 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: A 294 ILE cc_start: 0.9021 (mt) cc_final: 0.8795 (mt) REVERT: A 484 LEU cc_start: 0.9026 (tp) cc_final: 0.8713 (tt) REVERT: B 34 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: B 294 ILE cc_start: 0.9017 (mt) cc_final: 0.8815 (mt) REVERT: B 484 LEU cc_start: 0.9039 (tp) cc_final: 0.8721 (tt) outliers start: 21 outliers final: 17 residues processed: 131 average time/residue: 0.1525 time to fit residues: 28.7103 Evaluate side-chains 138 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 7 optimal weight: 0.0970 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7475 Z= 0.211 Angle : 0.652 11.181 10235 Z= 0.313 Chirality : 0.043 0.224 1252 Planarity : 0.005 0.066 1195 Dihedral : 4.942 30.128 1085 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.64 % Allowed : 17.38 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -0.41 (0.30), residues: 903 helix: 0.46 (0.23), residues: 643 sheet: None (None), residues: 0 loop : -2.01 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 PHE 0.013 0.001 PHE B 287 TYR 0.025 0.001 TYR B 514 ARG 0.002 0.000 ARG B 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.774 Fit side-chains REVERT: A 99 ILE cc_start: 0.8907 (tt) cc_final: 0.8651 (tt) REVERT: A 294 ILE cc_start: 0.9045 (mt) cc_final: 0.8832 (mt) REVERT: A 484 LEU cc_start: 0.9037 (tp) cc_final: 0.8716 (tt) REVERT: B 34 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: B 484 LEU cc_start: 0.9043 (tp) cc_final: 0.8729 (tt) outliers start: 21 outliers final: 19 residues processed: 131 average time/residue: 0.1571 time to fit residues: 29.3652 Evaluate side-chains 136 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.105410 restraints weight = 9219.381| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.58 r_work: 0.3011 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7475 Z= 0.207 Angle : 0.648 10.969 10235 Z= 0.312 Chirality : 0.043 0.223 1252 Planarity : 0.005 0.065 1195 Dihedral : 4.950 29.758 1085 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.77 % Allowed : 17.76 % Favored : 79.47 % 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: -0.37 (0.30), residues: 903 helix: 0.50 (0.23), residues: 642 sheet: None (None), residues: 0 loop : -2.04 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 572 HIS 0.007 0.001 HIS B 105 PHE 0.014 0.001 PHE B 287 TYR 0.010 0.001 TYR A 39 ARG 0.001 0.000 ARG B 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1694.35 seconds wall clock time: 31 minutes 36.18 seconds (1896.18 seconds total)