Starting phenix.real_space_refine on Sat Feb 17 17:22:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6p_25723/02_2024/7t6p_25723.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6p_25723/02_2024/7t6p_25723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6p_25723/02_2024/7t6p_25723.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6p_25723/02_2024/7t6p_25723.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6p_25723/02_2024/7t6p_25723.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6p_25723/02_2024/7t6p_25723.pdb" } resolution = 2.8 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= 0.001 sd= 0.055 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 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 9.49, per 1000 atoms: 0.49 Number of scatterers: 19412 At special positions: 0 Unit cell: (143.1, 143.1, 121.9, 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 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 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: 6.85 Conformation dependent library (CDL) restraints added in 3.9 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 8 sheets defined 65.3% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.740A pdb=" N ASP A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.882A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.940A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.655A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.653A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.096A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.769A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.917A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.816A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 306 through 309 removed outlier: 3.577A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 310 through 324 removed outlier: 4.108A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 380 through 410 Proline residue: A 405 - end of helix removed outlier: 3.826A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 4.388A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.660A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 510 removed outlier: 4.161A pdb=" N LEU A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.575A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.566A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 604 removed outlier: 3.833A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.780A pdb=" N ASP B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.881A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.958A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.642A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.573A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 removed outlier: 4.082A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 4.031A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.719A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.556A pdb=" N LEU B 234 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 231 through 235' Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.825A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 306 through 309 removed outlier: 3.571A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 310 through 324 removed outlier: 4.113A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 380 through 410 Proline residue: B 405 - end of helix removed outlier: 3.815A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 4.378A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.664A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 510 removed outlier: 4.132A pdb=" N LEU B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.624A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.528A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 604 removed outlier: 3.828A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.706A pdb=" N ASP C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.932A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.587A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.531A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.853A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 removed outlier: 4.105A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 206 " --> pdb=" O ILE C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.601A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.531A pdb=" N LEU C 234 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 235' Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 262 removed outlier: 4.001A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 306 through 309 removed outlier: 3.514A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 310 through 324 removed outlier: 4.204A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.682A pdb=" N TYR C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 410 Proline residue: C 405 - end of helix removed outlier: 3.828A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 4.558A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.648A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 510 removed outlier: 4.028A pdb=" N LEU C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.626A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 Processing helix chain 'C' and resid 569 through 604 removed outlier: 4.075A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.742A pdb=" N ASP D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.879A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.940A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.655A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.583A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 4.098A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 4.038A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 222 removed outlier: 3.729A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.550A pdb=" N LEU D 234 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 231 through 235' Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 263 removed outlier: 3.838A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 310 through 324 removed outlier: 4.085A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 380 through 410 Proline residue: D 405 - end of helix removed outlier: 3.803A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 4.378A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.664A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 510 removed outlier: 4.174A pdb=" N LEU D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.633A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.551A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 604 removed outlier: 3.849A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.837A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.852A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.809A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.851A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1060 hydrogen bonds defined for protein. 3135 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: 6.27 Time building geometry restraints manager: 7.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6103 1.34 - 1.46: 3961 1.46 - 1.58: 9568 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" C THR C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.23e-02 6.61e+03 1.40e+01 bond pdb=" C THR B 311 " pdb=" N PRO B 312 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.24e-02 6.50e+03 1.26e+01 bond pdb=" C THR A 311 " pdb=" N PRO A 312 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.24e-02 6.50e+03 1.25e+01 bond pdb=" CG1 ILE D 501 " pdb=" CD1 ILE D 501 " ideal model delta sigma weight residual 1.513 1.381 0.132 3.90e-02 6.57e+02 1.14e+01 bond pdb=" C THR D 311 " pdb=" N PRO D 312 " ideal model delta sigma weight residual 1.337 1.379 -0.042 1.24e-02 6.50e+03 1.13e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.58: 430 105.58 - 112.85: 10130 112.85 - 120.12: 8027 120.12 - 127.40: 8131 127.40 - 134.67: 246 Bond angle restraints: 26964 Sorted by residual: angle pdb=" C LEU D 604 " pdb=" N GLU D 605 " pdb=" CA GLU D 605 " ideal model delta sigma weight residual 121.54 133.71 -12.17 1.91e+00 2.74e-01 4.06e+01 angle pdb=" C LEU A 604 " pdb=" N GLU A 605 " pdb=" CA GLU A 605 " ideal model delta sigma weight residual 121.54 133.68 -12.14 1.91e+00 2.74e-01 4.04e+01 angle pdb=" C LEU B 604 " pdb=" N GLU B 605 " pdb=" CA GLU B 605 " ideal model delta sigma weight residual 121.54 133.64 -12.10 1.91e+00 2.74e-01 4.01e+01 angle pdb=" C VAL C 378 " pdb=" N THR C 379 " pdb=" CA THR C 379 " ideal model delta sigma weight residual 121.54 132.76 -11.22 1.91e+00 2.74e-01 3.45e+01 angle pdb=" C PRO B 362 " pdb=" N ARG B 363 " pdb=" CA ARG B 363 " ideal model delta sigma weight residual 121.54 132.41 -10.87 1.91e+00 2.74e-01 3.24e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 10391 15.92 - 31.84: 1060 31.84 - 47.75: 274 47.75 - 63.67: 59 63.67 - 79.59: 28 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA ILE A 510 " pdb=" C ILE A 510 " pdb=" N THR A 511 " pdb=" CA THR A 511 " ideal model delta harmonic sigma weight residual 180.00 146.06 33.94 0 5.00e+00 4.00e-02 4.61e+01 dihedral pdb=" CA ILE C 510 " pdb=" C ILE C 510 " pdb=" N THR C 511 " pdb=" CA THR C 511 " ideal model delta harmonic sigma weight residual 180.00 146.44 33.56 0 5.00e+00 4.00e-02 4.50e+01 dihedral pdb=" CA THR D 514 " pdb=" C THR D 514 " pdb=" N GLU D 515 " pdb=" CA GLU D 515 " ideal model delta harmonic sigma weight residual -180.00 -146.53 -33.47 0 5.00e+00 4.00e-02 4.48e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2699 0.088 - 0.175: 327 0.175 - 0.263: 32 0.263 - 0.350: 8 0.350 - 0.438: 6 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB THR C 379 " pdb=" CA THR C 379 " pdb=" OG1 THR C 379 " pdb=" CG2 THR C 379 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CB THR A 379 " pdb=" CA THR A 379 " pdb=" OG1 THR A 379 " pdb=" CG2 THR A 379 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CB THR B 379 " pdb=" CA THR B 379 " pdb=" OG1 THR B 379 " pdb=" CG2 THR B 379 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 511 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C THR D 511 " 0.048 2.00e-02 2.50e+03 pdb=" O THR D 511 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE D 512 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 585 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C VAL D 585 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL D 585 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA D 586 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 511 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C THR B 511 " 0.047 2.00e-02 2.50e+03 pdb=" O THR B 511 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE B 512 " -0.016 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5711 2.83 - 3.35: 17920 3.35 - 3.86: 33109 3.86 - 4.38: 39220 4.38 - 4.90: 65697 Nonbonded interactions: 161657 Sorted by model distance: nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.310 2.440 nonbonded pdb=" O LEU C 568 " pdb=" ND2 ASN C 572 " model vdw 2.368 2.520 nonbonded pdb=" O LEU D 568 " pdb=" ND2 ASN D 572 " model vdw 2.377 2.520 nonbonded pdb=" OE1 GLN A 73 " pdb=" NH1 ARG A 75 " model vdw 2.379 2.520 nonbonded pdb=" O LEU B 218 " pdb=" OG SER B 221 " model vdw 2.379 2.440 ... (remaining 161652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.950 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: 4.790 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 50.560 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 : 0.005 0.132 19860 Z= 0.343 Angle : 1.127 12.437 26964 Z= 0.596 Chirality : 0.061 0.438 3072 Planarity : 0.008 0.067 3416 Dihedral : 14.543 79.591 7236 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.37 (0.13), residues: 2408 helix: -2.24 (0.10), residues: 1444 sheet: -1.71 (0.51), residues: 64 loop : -1.97 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 583 HIS 0.008 0.001 HIS A 637 PHE 0.029 0.003 PHE C 456 TYR 0.039 0.002 TYR A 328 ARG 0.005 0.001 ARG C 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 2.431 Fit side-chains revert: symmetry clash REVERT: A 51 GLN cc_start: 0.7699 (tp-100) cc_final: 0.7494 (tp-100) REVERT: A 55 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 257 GLN cc_start: 0.7004 (mm110) cc_final: 0.6578 (tp40) REVERT: A 497 MET cc_start: 0.7923 (ttt) cc_final: 0.7676 (ttt) REVERT: A 515 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6113 (mm-30) REVERT: A 583 TRP cc_start: 0.8131 (p-90) cc_final: 0.7877 (p-90) REVERT: B 51 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7467 (tp-100) REVERT: B 55 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 257 GLN cc_start: 0.7030 (mm110) cc_final: 0.6720 (mm110) REVERT: B 429 ILE cc_start: 0.7628 (mt) cc_final: 0.7377 (tp) REVERT: B 447 MET cc_start: 0.7461 (mtm) cc_final: 0.7190 (ptm) REVERT: C 51 GLN cc_start: 0.7702 (tp-100) cc_final: 0.7482 (tp-100) REVERT: C 55 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7653 (mt-10) REVERT: C 181 LEU cc_start: 0.8399 (tt) cc_final: 0.8170 (tm) REVERT: C 239 GLN cc_start: 0.8047 (tt0) cc_final: 0.7828 (tt0) REVERT: D 257 GLN cc_start: 0.7158 (mm110) cc_final: 0.6939 (mm110) REVERT: D 260 MET cc_start: 0.7342 (mmp) cc_final: 0.7080 (mmt) REVERT: D 447 MET cc_start: 0.7485 (mtm) cc_final: 0.7242 (ptm) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 1.1484 time to fit residues: 540.6958 Evaluate side-chains 316 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 0.2980 chunk 217 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 261 GLN A 374 GLN A 380 HIS B 185 HIS B 261 GLN B 374 GLN B 380 HIS C 185 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 374 GLN D 185 HIS D 261 GLN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN D 380 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19860 Z= 0.232 Angle : 0.628 10.112 26964 Z= 0.323 Chirality : 0.042 0.243 3072 Planarity : 0.005 0.047 3416 Dihedral : 4.929 22.991 2644 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.62 % Allowed : 11.35 % Favored : 86.02 % 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: -1.46 (0.15), residues: 2408 helix: -0.37 (0.12), residues: 1484 sheet: -2.18 (0.46), residues: 84 loop : -1.77 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 583 HIS 0.004 0.001 HIS D 201 PHE 0.021 0.001 PHE B 611 TYR 0.015 0.001 TYR B 555 ARG 0.005 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 326 time to evaluate : 2.475 Fit side-chains REVERT: A 51 GLN cc_start: 0.7825 (tp-100) cc_final: 0.7492 (tp-100) REVERT: A 55 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7493 (mt-10) REVERT: A 214 GLN cc_start: 0.7708 (mp10) cc_final: 0.7155 (mp10) REVERT: A 349 TYR cc_start: 0.8376 (m-80) cc_final: 0.8106 (m-80) REVERT: A 381 GLN cc_start: 0.7348 (mp10) cc_final: 0.6427 (mt0) REVERT: A 497 MET cc_start: 0.8042 (ttt) cc_final: 0.7758 (ttt) REVERT: B 51 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7508 (tp-100) REVERT: B 55 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7453 (mt-10) REVERT: B 214 GLN cc_start: 0.7535 (mp10) cc_final: 0.7105 (mp10) REVERT: B 294 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7229 (mt-10) REVERT: B 349 TYR cc_start: 0.8358 (m-80) cc_final: 0.8133 (m-80) REVERT: B 381 GLN cc_start: 0.7319 (mp10) cc_final: 0.6384 (mt0) REVERT: C 51 GLN cc_start: 0.7842 (tp-100) cc_final: 0.7527 (tp-100) REVERT: C 55 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7488 (mt-10) REVERT: C 62 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7792 (mttt) REVERT: C 214 GLN cc_start: 0.7672 (mp10) cc_final: 0.7093 (mp10) REVERT: C 215 MET cc_start: 0.8895 (mmm) cc_final: 0.8634 (tpp) REVERT: C 239 GLN cc_start: 0.8321 (tt0) cc_final: 0.8111 (tt0) REVERT: C 349 TYR cc_start: 0.8466 (m-80) cc_final: 0.8258 (m-80) REVERT: C 372 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7066 (mt) REVERT: C 497 MET cc_start: 0.7972 (ttt) cc_final: 0.7572 (ttt) REVERT: D 55 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7742 (mt-10) REVERT: D 214 GLN cc_start: 0.7535 (mp10) cc_final: 0.7116 (mp10) REVERT: D 381 GLN cc_start: 0.7327 (mp10) cc_final: 0.6401 (mt0) outliers start: 55 outliers final: 15 residues processed: 349 average time/residue: 1.0968 time to fit residues: 440.1256 Evaluate side-chains 305 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 289 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 218 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 216 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 310 GLN A 374 GLN A 380 HIS B 73 GLN B 261 GLN B 310 GLN B 374 GLN B 380 HIS C 73 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 374 GLN D 73 GLN D 128 GLN D 261 GLN D 310 GLN D 369 GLN D 374 GLN D 380 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19860 Z= 0.232 Angle : 0.591 7.338 26964 Z= 0.305 Chirality : 0.041 0.286 3072 Planarity : 0.005 0.049 3416 Dihedral : 4.701 25.929 2644 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.10 % Allowed : 14.74 % Favored : 82.16 % 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: -0.56 (0.16), residues: 2408 helix: 0.47 (0.13), residues: 1488 sheet: -1.96 (0.43), residues: 104 loop : -1.63 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 583 HIS 0.004 0.001 HIS D 201 PHE 0.011 0.001 PHE D 523 TYR 0.011 0.001 TYR A 328 ARG 0.003 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 308 time to evaluate : 2.247 Fit side-chains REVERT: A 51 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7599 (tp-100) REVERT: A 55 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 214 GLN cc_start: 0.7902 (mp10) cc_final: 0.7228 (mp10) REVERT: A 257 GLN cc_start: 0.6941 (mm-40) cc_final: 0.6713 (tp40) REVERT: A 315 GLU cc_start: 0.8058 (mp0) cc_final: 0.7630 (mp0) REVERT: A 349 TYR cc_start: 0.8356 (m-80) cc_final: 0.8072 (m-80) REVERT: A 381 GLN cc_start: 0.7198 (mp10) cc_final: 0.6324 (mt0) REVERT: A 429 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7369 (tp) REVERT: A 497 MET cc_start: 0.8005 (ttt) cc_final: 0.7794 (ttt) REVERT: B 51 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7600 (tp-100) REVERT: B 55 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7555 (mt-10) REVERT: B 214 GLN cc_start: 0.7619 (mp10) cc_final: 0.7145 (mp10) REVERT: B 315 GLU cc_start: 0.8042 (mp0) cc_final: 0.7631 (mp0) REVERT: B 349 TYR cc_start: 0.8362 (m-80) cc_final: 0.8094 (m-80) REVERT: B 381 GLN cc_start: 0.7199 (mp10) cc_final: 0.6328 (mt0) REVERT: C 51 GLN cc_start: 0.7842 (tp-100) cc_final: 0.7601 (tp-100) REVERT: C 55 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7556 (mt-10) REVERT: C 62 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7939 (mttt) REVERT: C 214 GLN cc_start: 0.7684 (mp10) cc_final: 0.7062 (mp10) REVERT: C 257 GLN cc_start: 0.7257 (mm-40) cc_final: 0.7052 (mm110) REVERT: C 315 GLU cc_start: 0.7955 (mp0) cc_final: 0.7361 (mp0) REVERT: C 497 MET cc_start: 0.8099 (ttt) cc_final: 0.7708 (ttt) REVERT: D 55 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7768 (mt-10) REVERT: D 99 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.5578 (mpp) REVERT: D 214 GLN cc_start: 0.7596 (mp10) cc_final: 0.7145 (mp10) REVERT: D 349 TYR cc_start: 0.8348 (m-80) cc_final: 0.8102 (m-80) REVERT: D 381 GLN cc_start: 0.7226 (mp10) cc_final: 0.6333 (mt0) outliers start: 65 outliers final: 19 residues processed: 348 average time/residue: 1.2083 time to fit residues: 478.0042 Evaluate side-chains 292 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 271 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 372 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 0.6980 chunk 231 optimal weight: 0.0370 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 374 GLN A 380 HIS ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 374 GLN B 380 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 374 GLN C 637 HIS D 261 GLN D 374 GLN D 380 HIS D 635 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19860 Z= 0.164 Angle : 0.567 9.514 26964 Z= 0.287 Chirality : 0.040 0.291 3072 Planarity : 0.004 0.046 3416 Dihedral : 4.463 25.499 2644 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.58 % Allowed : 17.94 % Favored : 79.48 % 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: -0.03 (0.17), residues: 2408 helix: 0.90 (0.14), residues: 1492 sheet: -1.97 (0.44), residues: 104 loop : -1.44 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 583 HIS 0.003 0.001 HIS C 637 PHE 0.020 0.001 PHE D 611 TYR 0.012 0.001 TYR D 328 ARG 0.004 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 300 time to evaluate : 2.210 Fit side-chains REVERT: A 51 GLN cc_start: 0.7956 (tp-100) cc_final: 0.7604 (tp-100) REVERT: A 55 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7536 (mt-10) REVERT: A 99 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.5561 (mpp) REVERT: A 100 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: A 214 GLN cc_start: 0.7696 (mp10) cc_final: 0.7067 (mp10) REVERT: A 294 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7068 (mt-10) REVERT: A 315 GLU cc_start: 0.7973 (mp0) cc_final: 0.7503 (mp0) REVERT: A 318 SER cc_start: 0.8157 (m) cc_final: 0.7898 (t) REVERT: A 349 TYR cc_start: 0.8313 (m-80) cc_final: 0.8099 (m-80) REVERT: A 429 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7334 (tp) REVERT: A 497 MET cc_start: 0.7872 (ttt) cc_final: 0.7540 (ttt) REVERT: B 51 GLN cc_start: 0.7958 (tp-100) cc_final: 0.7605 (tp-100) REVERT: B 55 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 100 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7821 (pt0) REVERT: B 214 GLN cc_start: 0.7720 (mp10) cc_final: 0.7213 (mp10) REVERT: B 315 GLU cc_start: 0.7969 (mp0) cc_final: 0.7500 (mp0) REVERT: B 318 SER cc_start: 0.8244 (m) cc_final: 0.7970 (t) REVERT: B 349 TYR cc_start: 0.8317 (m-80) cc_final: 0.8115 (m-80) REVERT: B 528 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7793 (p) REVERT: C 51 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7463 (tp-100) REVERT: C 55 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7490 (mt-10) REVERT: C 62 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7912 (mttt) REVERT: C 214 GLN cc_start: 0.7686 (mp10) cc_final: 0.7128 (mp10) REVERT: C 257 GLN cc_start: 0.7333 (mm-40) cc_final: 0.7118 (mm110) REVERT: C 294 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7070 (mt-10) REVERT: C 315 GLU cc_start: 0.7719 (mp0) cc_final: 0.7372 (mp0) REVERT: C 318 SER cc_start: 0.8240 (m) cc_final: 0.7951 (t) REVERT: C 379 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7878 (p) REVERT: C 451 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7930 (t) REVERT: C 497 MET cc_start: 0.8053 (ttt) cc_final: 0.7646 (ttt) REVERT: D 55 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7696 (mt-10) REVERT: D 99 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.5563 (mpp) REVERT: D 214 GLN cc_start: 0.7689 (mp10) cc_final: 0.7196 (mp10) REVERT: D 318 SER cc_start: 0.8161 (m) cc_final: 0.7909 (t) REVERT: D 349 TYR cc_start: 0.8325 (m-80) cc_final: 0.8005 (m-80) REVERT: D 429 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7195 (tp) REVERT: D 528 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7754 (p) outliers start: 54 outliers final: 16 residues processed: 326 average time/residue: 1.1881 time to fit residues: 441.2999 Evaluate side-chains 296 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 270 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 528 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 208 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 261 GLN A 374 GLN A 380 HIS A 635 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 374 GLN B 380 HIS B 635 ASN C 74 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN C 637 HIS D 261 GLN D 374 GLN D 380 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19860 Z= 0.199 Angle : 0.573 11.920 26964 Z= 0.289 Chirality : 0.041 0.238 3072 Planarity : 0.004 0.046 3416 Dihedral : 4.408 25.613 2644 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.53 % Allowed : 18.70 % Favored : 77.77 % 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: 0.21 (0.17), residues: 2408 helix: 1.09 (0.14), residues: 1496 sheet: -1.94 (0.44), residues: 104 loop : -1.34 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 583 HIS 0.003 0.001 HIS C 637 PHE 0.019 0.001 PHE D 611 TYR 0.011 0.001 TYR C 328 ARG 0.009 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 288 time to evaluate : 2.314 Fit side-chains revert: symmetry clash REVERT: A 51 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7571 (tp-100) REVERT: A 55 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 100 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7745 (pt0) REVERT: A 214 GLN cc_start: 0.7631 (mp10) cc_final: 0.7061 (mp10) REVERT: A 294 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7113 (mt-10) REVERT: A 315 GLU cc_start: 0.8024 (mp0) cc_final: 0.7557 (mp0) REVERT: A 318 SER cc_start: 0.8153 (m) cc_final: 0.7922 (t) REVERT: A 349 TYR cc_start: 0.8314 (m-80) cc_final: 0.7999 (m-80) REVERT: A 429 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7339 (tp) REVERT: A 447 MET cc_start: 0.7690 (ptm) cc_final: 0.7459 (ptp) REVERT: A 497 MET cc_start: 0.7835 (ttt) cc_final: 0.7545 (ttt) REVERT: B 51 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7568 (tp-100) REVERT: B 55 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7516 (mt-10) REVERT: B 99 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.5671 (mpp) REVERT: B 100 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: B 214 GLN cc_start: 0.7651 (mp10) cc_final: 0.7115 (mp10) REVERT: B 315 GLU cc_start: 0.8032 (mp0) cc_final: 0.7542 (mp0) REVERT: B 318 SER cc_start: 0.8243 (m) cc_final: 0.7995 (t) REVERT: B 349 TYR cc_start: 0.8316 (m-80) cc_final: 0.8081 (m-80) REVERT: B 501 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8322 (mm) REVERT: B 528 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7761 (p) REVERT: C 51 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7459 (tp-100) REVERT: C 55 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7483 (mt-10) REVERT: C 62 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7927 (mttt) REVERT: C 214 GLN cc_start: 0.7759 (mp10) cc_final: 0.7187 (mp10) REVERT: C 257 GLN cc_start: 0.7334 (mm-40) cc_final: 0.7133 (mm110) REVERT: C 294 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7089 (mt-10) REVERT: C 315 GLU cc_start: 0.7810 (mp0) cc_final: 0.7430 (mp0) REVERT: C 318 SER cc_start: 0.8244 (m) cc_final: 0.7978 (t) REVERT: C 379 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7818 (p) REVERT: C 451 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7997 (t) REVERT: C 497 MET cc_start: 0.7948 (ttt) cc_final: 0.7580 (ttt) REVERT: D 55 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7845 (mt-10) REVERT: D 99 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.5526 (mpp) REVERT: D 100 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: D 214 GLN cc_start: 0.7580 (mp10) cc_final: 0.7075 (mp10) REVERT: D 294 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7142 (mt-10) REVERT: D 318 SER cc_start: 0.8145 (m) cc_final: 0.7907 (t) REVERT: D 349 TYR cc_start: 0.8301 (m-80) cc_final: 0.8078 (m-80) REVERT: D 372 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7322 (mt) REVERT: D 429 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7209 (tp) REVERT: D 528 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7738 (p) outliers start: 74 outliers final: 30 residues processed: 332 average time/residue: 1.1947 time to fit residues: 450.6839 Evaluate side-chains 311 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 268 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 434 SER Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.7980 chunk 208 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 0.1980 chunk 121 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 261 GLN A 310 GLN A 374 GLN A 380 HIS B 261 GLN B 374 GLN B 380 HIS B 637 HIS C 73 GLN C 74 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN D 261 GLN D 374 GLN D 380 HIS D 637 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19860 Z= 0.177 Angle : 0.561 11.485 26964 Z= 0.282 Chirality : 0.040 0.175 3072 Planarity : 0.004 0.046 3416 Dihedral : 4.345 25.539 2644 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.53 % Allowed : 19.27 % Favored : 77.19 % 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: 0.40 (0.17), residues: 2408 helix: 1.24 (0.14), residues: 1492 sheet: -1.93 (0.44), residues: 104 loop : -1.25 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 583 HIS 0.003 0.001 HIS D 637 PHE 0.017 0.001 PHE D 611 TYR 0.012 0.001 TYR C 328 ARG 0.009 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 282 time to evaluate : 2.439 Fit side-chains REVERT: A 51 GLN cc_start: 0.7845 (tp-100) cc_final: 0.7463 (tp-100) REVERT: A 55 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 99 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.5545 (mpp) REVERT: A 214 GLN cc_start: 0.7706 (mp10) cc_final: 0.7133 (mp10) REVERT: A 294 GLU cc_start: 0.7271 (mt-10) cc_final: 0.7069 (mt-10) REVERT: A 315 GLU cc_start: 0.8005 (mp0) cc_final: 0.7538 (mp0) REVERT: A 318 SER cc_start: 0.8148 (m) cc_final: 0.7932 (t) REVERT: A 349 TYR cc_start: 0.8321 (m-80) cc_final: 0.8075 (m-80) REVERT: A 447 MET cc_start: 0.7695 (ptm) cc_final: 0.7454 (ptp) REVERT: A 497 MET cc_start: 0.7763 (ttt) cc_final: 0.7480 (ttt) REVERT: B 51 GLN cc_start: 0.7873 (tp-100) cc_final: 0.7494 (tp-100) REVERT: B 55 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7432 (mt-10) REVERT: B 99 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.5601 (mpp) REVERT: B 100 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7776 (pt0) REVERT: B 214 GLN cc_start: 0.7650 (mp10) cc_final: 0.7184 (mp10) REVERT: B 315 GLU cc_start: 0.8006 (mp0) cc_final: 0.7510 (mp0) REVERT: B 318 SER cc_start: 0.8238 (m) cc_final: 0.8002 (t) REVERT: B 349 TYR cc_start: 0.8325 (m-80) cc_final: 0.8089 (m-80) REVERT: B 451 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.8061 (t) REVERT: B 528 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7758 (p) REVERT: C 51 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7600 (tp-100) REVERT: C 55 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7573 (mt-10) REVERT: C 62 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7918 (mttt) REVERT: C 97 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7562 (mm) REVERT: C 99 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.5599 (mpp) REVERT: C 294 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7065 (mt-10) REVERT: C 315 GLU cc_start: 0.7738 (mp0) cc_final: 0.7381 (mp0) REVERT: C 318 SER cc_start: 0.8267 (m) cc_final: 0.7997 (t) REVERT: C 429 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7205 (tp) REVERT: C 451 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7996 (t) REVERT: C 497 MET cc_start: 0.7828 (ttt) cc_final: 0.7511 (ttt) REVERT: D 55 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7862 (mt-10) REVERT: D 99 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.5523 (mpp) REVERT: D 100 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: D 214 GLN cc_start: 0.7657 (mp10) cc_final: 0.7208 (mp10) REVERT: D 294 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7088 (mt-10) REVERT: D 318 SER cc_start: 0.8150 (m) cc_final: 0.7908 (t) REVERT: D 349 TYR cc_start: 0.8315 (m-80) cc_final: 0.7960 (m-80) REVERT: D 372 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7352 (mt) REVERT: D 528 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7747 (p) outliers start: 74 outliers final: 26 residues processed: 330 average time/residue: 1.2161 time to fit residues: 459.4609 Evaluate side-chains 308 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 269 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 434 SER Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 195 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 231 optimal weight: 0.3980 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 374 GLN A 380 HIS B 261 GLN B 374 GLN B 380 HIS C 73 GLN C 74 GLN C 128 GLN C 257 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN D 261 GLN D 374 GLN D 380 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 19860 Z= 0.245 Angle : 0.606 11.996 26964 Z= 0.306 Chirality : 0.043 0.365 3072 Planarity : 0.004 0.046 3416 Dihedral : 4.454 25.846 2644 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.24 % Allowed : 20.32 % Favored : 76.43 % 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: 0.45 (0.17), residues: 2408 helix: 1.26 (0.14), residues: 1488 sheet: -1.92 (0.45), residues: 104 loop : -1.15 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 286 HIS 0.004 0.001 HIS C 582 PHE 0.018 0.001 PHE D 611 TYR 0.013 0.001 TYR C 328 ARG 0.010 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 283 time to evaluate : 2.371 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 99 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.5543 (mpp) REVERT: A 294 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7167 (mt-10) REVERT: A 315 GLU cc_start: 0.8023 (mp0) cc_final: 0.7431 (mp0) REVERT: A 349 TYR cc_start: 0.8322 (m-80) cc_final: 0.8064 (m-80) REVERT: A 497 MET cc_start: 0.7938 (ttt) cc_final: 0.7624 (ttt) REVERT: A 501 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8323 (mm) REVERT: B 51 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7690 (tp-100) REVERT: B 55 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 99 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.5612 (mpp) REVERT: B 260 MET cc_start: 0.7469 (mmt) cc_final: 0.7201 (mmt) REVERT: B 315 GLU cc_start: 0.8036 (mp0) cc_final: 0.7492 (mp0) REVERT: B 318 SER cc_start: 0.8160 (m) cc_final: 0.7948 (t) REVERT: B 349 TYR cc_start: 0.8322 (m-80) cc_final: 0.8070 (m-80) REVERT: B 528 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7733 (p) REVERT: B 569 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7848 (tp) REVERT: C 51 GLN cc_start: 0.7871 (tp-100) cc_final: 0.7570 (tp-100) REVERT: C 55 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7488 (mt-10) REVERT: C 62 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7937 (mttt) REVERT: C 97 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7569 (mm) REVERT: C 99 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.5626 (mpp) REVERT: C 214 GLN cc_start: 0.7933 (mp10) cc_final: 0.7678 (mp10) REVERT: C 294 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7168 (mt-10) REVERT: C 315 GLU cc_start: 0.7793 (mp0) cc_final: 0.7317 (mp0) REVERT: C 318 SER cc_start: 0.8164 (m) cc_final: 0.7946 (t) REVERT: C 429 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7225 (tp) REVERT: C 451 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.8018 (t) REVERT: C 497 MET cc_start: 0.7997 (ttt) cc_final: 0.7701 (ttt) REVERT: C 501 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8309 (mm) REVERT: D 55 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7801 (mt-10) REVERT: D 99 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.5679 (mpp) REVERT: D 294 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7053 (mt-10) REVERT: D 318 SER cc_start: 0.8151 (m) cc_final: 0.7928 (t) REVERT: D 349 TYR cc_start: 0.8307 (m-80) cc_final: 0.7945 (m-80) REVERT: D 528 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7714 (p) outliers start: 68 outliers final: 27 residues processed: 322 average time/residue: 1.2194 time to fit residues: 445.2926 Evaluate side-chains 312 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 273 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 434 SER Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 548 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 147 optimal weight: 0.4980 chunk 157 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 181 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 374 GLN A 380 HIS B 261 GLN B 374 GLN B 380 HIS B 637 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 370 GLN C 374 GLN D 261 GLN D 374 GLN D 380 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19860 Z= 0.173 Angle : 0.577 12.343 26964 Z= 0.289 Chirality : 0.041 0.358 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.352 25.783 2644 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.43 % Allowed : 21.28 % Favored : 76.29 % 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: 0.60 (0.18), residues: 2408 helix: 1.36 (0.14), residues: 1488 sheet: -1.88 (0.45), residues: 104 loop : -1.05 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 583 HIS 0.003 0.001 HIS B 637 PHE 0.016 0.001 PHE D 611 TYR 0.010 0.001 TYR D 555 ARG 0.010 0.000 ARG C 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 284 time to evaluate : 2.156 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7787 (mt-10) REVERT: A 99 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.5552 (mpp) REVERT: A 214 GLN cc_start: 0.7892 (mp10) cc_final: 0.7631 (mp10) REVERT: A 294 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7107 (mt-10) REVERT: A 315 GLU cc_start: 0.7996 (mp0) cc_final: 0.7512 (mp0) REVERT: A 349 TYR cc_start: 0.8299 (m-80) cc_final: 0.8045 (m-80) REVERT: A 447 MET cc_start: 0.7664 (ptm) cc_final: 0.7399 (ptp) REVERT: A 497 MET cc_start: 0.7922 (ttt) cc_final: 0.7587 (ttt) REVERT: B 51 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7580 (tp-100) REVERT: B 55 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7448 (mt-10) REVERT: B 99 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.5513 (mpp) REVERT: B 214 GLN cc_start: 0.7878 (mp10) cc_final: 0.7182 (mp10) REVERT: B 315 GLU cc_start: 0.8021 (mp0) cc_final: 0.7511 (mp0) REVERT: B 318 SER cc_start: 0.8217 (m) cc_final: 0.8000 (t) REVERT: B 349 TYR cc_start: 0.8283 (m-80) cc_final: 0.8053 (m-80) REVERT: B 381 GLN cc_start: 0.7257 (mp10) cc_final: 0.6281 (mt0) REVERT: B 528 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7783 (p) REVERT: C 31 GLN cc_start: 0.7371 (pt0) cc_final: 0.7163 (pt0) REVERT: C 51 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7608 (tp-100) REVERT: C 55 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7551 (mt-10) REVERT: C 62 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7913 (mttt) REVERT: C 97 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7510 (mm) REVERT: C 99 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.5620 (mpp) REVERT: C 214 GLN cc_start: 0.7869 (mp10) cc_final: 0.7528 (mp10) REVERT: C 294 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7097 (mt-10) REVERT: C 315 GLU cc_start: 0.7691 (mp0) cc_final: 0.7366 (mp0) REVERT: C 318 SER cc_start: 0.8150 (m) cc_final: 0.7930 (t) REVERT: C 429 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7205 (tp) REVERT: C 497 MET cc_start: 0.7949 (ttt) cc_final: 0.7648 (ttt) REVERT: D 55 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7791 (mt-10) REVERT: D 214 GLN cc_start: 0.7879 (mp10) cc_final: 0.7525 (mp10) REVERT: D 294 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7096 (mt-10) REVERT: D 318 SER cc_start: 0.8216 (m) cc_final: 0.7986 (t) REVERT: D 349 TYR cc_start: 0.8248 (m-80) cc_final: 0.7912 (m-80) REVERT: D 381 GLN cc_start: 0.7208 (mp10) cc_final: 0.6177 (mt0) REVERT: D 528 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7761 (p) outliers start: 51 outliers final: 22 residues processed: 315 average time/residue: 1.2294 time to fit residues: 439.2545 Evaluate side-chains 297 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 268 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 169 optimal weight: 0.4980 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 374 GLN A 637 HIS B 261 GLN B 374 GLN B 637 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 374 GLN D 261 GLN D 374 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19860 Z= 0.214 Angle : 0.604 12.724 26964 Z= 0.300 Chirality : 0.042 0.320 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.382 26.050 2644 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.24 % Allowed : 22.19 % Favored : 75.57 % 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: 0.60 (0.18), residues: 2408 helix: 1.32 (0.14), residues: 1492 sheet: -1.90 (0.45), residues: 104 loop : -0.98 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 583 HIS 0.003 0.001 HIS A 637 PHE 0.016 0.001 PHE D 611 TYR 0.015 0.001 TYR C 328 ARG 0.010 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 270 time to evaluate : 2.240 Fit side-chains REVERT: A 55 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 99 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.5619 (mpp) REVERT: A 214 GLN cc_start: 0.7889 (mp10) cc_final: 0.7574 (mp10) REVERT: A 294 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7108 (mt-10) REVERT: A 315 GLU cc_start: 0.8019 (mp0) cc_final: 0.7497 (mp0) REVERT: A 349 TYR cc_start: 0.8302 (m-80) cc_final: 0.8041 (m-80) REVERT: A 569 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7854 (tp) REVERT: B 55 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7620 (mt-10) REVERT: B 99 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.5662 (mpp) REVERT: B 214 GLN cc_start: 0.7890 (mp10) cc_final: 0.7601 (mp10) REVERT: B 315 GLU cc_start: 0.8010 (mp0) cc_final: 0.7518 (mp0) REVERT: B 318 SER cc_start: 0.8217 (m) cc_final: 0.8009 (t) REVERT: B 349 TYR cc_start: 0.8307 (m-80) cc_final: 0.8061 (m-80) REVERT: B 381 GLN cc_start: 0.7295 (mp10) cc_final: 0.6297 (mt0) REVERT: B 528 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7758 (p) REVERT: C 31 GLN cc_start: 0.7379 (pt0) cc_final: 0.7167 (pt0) REVERT: C 51 GLN cc_start: 0.7863 (tp-100) cc_final: 0.7545 (tp-100) REVERT: C 55 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7462 (mt-10) REVERT: C 62 LYS cc_start: 0.8303 (mtmm) cc_final: 0.7934 (mttt) REVERT: C 97 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7549 (mm) REVERT: C 99 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.5647 (mpp) REVERT: C 214 GLN cc_start: 0.7879 (mp10) cc_final: 0.7678 (mp10) REVERT: C 294 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7100 (mt-10) REVERT: C 315 GLU cc_start: 0.7730 (mp0) cc_final: 0.7353 (mp0) REVERT: C 318 SER cc_start: 0.8167 (m) cc_final: 0.7944 (t) REVERT: C 429 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7215 (tp) REVERT: C 497 MET cc_start: 0.8108 (ttt) cc_final: 0.7793 (ttt) REVERT: D 55 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7794 (mt-10) REVERT: D 214 GLN cc_start: 0.7871 (mp10) cc_final: 0.7615 (mp10) REVERT: D 294 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7093 (mt-10) REVERT: D 318 SER cc_start: 0.8152 (m) cc_final: 0.7919 (t) REVERT: D 349 TYR cc_start: 0.8296 (m-80) cc_final: 0.7949 (m-80) REVERT: D 381 GLN cc_start: 0.7315 (mp10) cc_final: 0.6315 (mt0) REVERT: D 528 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7743 (p) REVERT: D 569 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7777 (tp) outliers start: 47 outliers final: 25 residues processed: 297 average time/residue: 1.3132 time to fit residues: 439.0645 Evaluate side-chains 295 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 261 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 434 SER Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 569 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.6980 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 239 optimal weight: 5.9990 chunk 220 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 374 GLN A 637 HIS B 261 GLN B 374 GLN B 637 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 374 GLN D 261 GLN D 374 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 19860 Z= 0.194 Angle : 0.596 12.650 26964 Z= 0.297 Chirality : 0.042 0.314 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.353 25.764 2644 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.24 % Allowed : 22.33 % Favored : 75.43 % 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: 0.62 (0.18), residues: 2408 helix: 1.34 (0.14), residues: 1488 sheet: -1.89 (0.45), residues: 104 loop : -0.97 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 583 HIS 0.003 0.001 HIS A 637 PHE 0.015 0.001 PHE D 611 TYR 0.014 0.001 TYR C 328 ARG 0.010 0.000 ARG D 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 276 time to evaluate : 2.346 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7800 (mt-10) REVERT: A 99 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.5583 (mpp) REVERT: A 214 GLN cc_start: 0.7843 (mp10) cc_final: 0.7514 (mp10) REVERT: A 294 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 315 GLU cc_start: 0.8001 (mp0) cc_final: 0.7501 (mp0) REVERT: A 349 TYR cc_start: 0.8265 (m-80) cc_final: 0.7968 (m-80) REVERT: A 569 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7840 (tp) REVERT: B 55 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 99 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.5686 (mpp) REVERT: B 214 GLN cc_start: 0.7865 (mp10) cc_final: 0.7595 (mp10) REVERT: B 315 GLU cc_start: 0.7994 (mp0) cc_final: 0.7474 (mp0) REVERT: B 318 SER cc_start: 0.8215 (m) cc_final: 0.8004 (t) REVERT: B 349 TYR cc_start: 0.8267 (m-80) cc_final: 0.8043 (m-80) REVERT: B 381 GLN cc_start: 0.7266 (mp10) cc_final: 0.6275 (mt0) REVERT: B 528 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7778 (p) REVERT: C 31 GLN cc_start: 0.7311 (pt0) cc_final: 0.7087 (pt0) REVERT: C 46 ASP cc_start: 0.8100 (m-30) cc_final: 0.7700 (m-30) REVERT: C 51 GLN cc_start: 0.7863 (tp-100) cc_final: 0.7542 (tp-100) REVERT: C 55 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7456 (mt-10) REVERT: C 62 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7943 (mttt) REVERT: C 97 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7533 (mm) REVERT: C 99 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.5660 (mpp) REVERT: C 214 GLN cc_start: 0.7894 (mp10) cc_final: 0.7685 (mp10) REVERT: C 261 GLN cc_start: 0.7795 (mm110) cc_final: 0.7473 (mm-40) REVERT: C 294 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7063 (mt-10) REVERT: C 315 GLU cc_start: 0.7694 (mp0) cc_final: 0.7359 (mp0) REVERT: C 318 SER cc_start: 0.8154 (m) cc_final: 0.7933 (t) REVERT: C 497 MET cc_start: 0.8114 (ttt) cc_final: 0.7847 (ttt) REVERT: D 55 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7843 (mt-10) REVERT: D 173 VAL cc_start: 0.8157 (OUTLIER) cc_final: 0.7947 (p) REVERT: D 214 GLN cc_start: 0.7763 (mp10) cc_final: 0.7499 (mp10) REVERT: D 294 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7161 (mt-10) REVERT: D 318 SER cc_start: 0.8239 (m) cc_final: 0.8003 (t) REVERT: D 349 TYR cc_start: 0.8234 (m-80) cc_final: 0.7913 (m-80) REVERT: D 381 GLN cc_start: 0.7296 (mp10) cc_final: 0.6274 (mt0) REVERT: D 528 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7758 (p) outliers start: 47 outliers final: 26 residues processed: 305 average time/residue: 1.3359 time to fit residues: 458.7234 Evaluate side-chains 299 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 265 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 434 SER Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 58 optimal weight: 0.1980 chunk 175 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 79 optimal weight: 0.0970 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 374 GLN B 261 GLN B 374 GLN B 637 HIS ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 374 GLN D 261 GLN D 374 GLN D 637 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.152486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114791 restraints weight = 23318.501| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.40 r_work: 0.3207 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19860 Z= 0.169 Angle : 0.586 12.714 26964 Z= 0.290 Chirality : 0.041 0.302 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.272 25.649 2644 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.00 % Allowed : 22.52 % 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: 0.69 (0.18), residues: 2408 helix: 1.36 (0.14), residues: 1496 sheet: -1.85 (0.45), residues: 104 loop : -0.87 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 583 HIS 0.003 0.001 HIS B 637 PHE 0.015 0.001 PHE D 611 TYR 0.016 0.001 TYR B 328 ARG 0.010 0.000 ARG A 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7207.48 seconds wall clock time: 129 minutes 15.72 seconds (7755.72 seconds total)