Starting phenix.real_space_refine on Mon Mar 18 21:26:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s88_24890/03_2024/7s88_24890.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s88_24890/03_2024/7s88_24890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s88_24890/03_2024/7s88_24890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s88_24890/03_2024/7s88_24890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s88_24890/03_2024/7s88_24890.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s88_24890/03_2024/7s88_24890.pdb" } resolution = 2.69 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= 0.025 sd= 0.215 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 32 5.49 5 S 160 5.16 5 C 14692 2.51 5 N 3392 2.21 5 O 3924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 621": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 621": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22201 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4935 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "B" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4935 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "C" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4935 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "D" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4935 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "A" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 580 Unusual residues: {' CA': 1, 'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 579 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 579 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 62 Chain: "D" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 579 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 62 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Time building chain proxies: 11.33, per 1000 atoms: 0.51 Number of scatterers: 22201 At special positions: 0 Unit cell: (133.147, 133.147, 122.396, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 160 16.00 P 32 15.00 O 3924 8.00 N 3392 7.00 C 14692 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: 7.86 Conformation dependent library (CDL) restraints added in 3.5 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 66.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 24 through 47 removed outlier: 3.532A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.678A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.541A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.103A pdb=" N GLU A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.540A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.868A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.591A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.569A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.786A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.556A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.072A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 414 through 423 removed outlier: 3.573A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.625A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.520A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 488 through 512 removed outlier: 5.169A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.140A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.548A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 removed outlier: 3.518A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 47 removed outlier: 3.531A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.678A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.542A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.104A pdb=" N GLU B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.540A 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 173 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.868A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.592A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.569A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.787A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.557A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.074A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 414 through 423 removed outlier: 3.572A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.625A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.520A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 488 through 512 removed outlier: 5.170A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.140A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.548A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 removed outlier: 3.518A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 47 removed outlier: 3.531A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.678A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.542A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.104A pdb=" N GLU C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.539A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.867A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.592A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.569A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.786A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.556A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.073A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 414 through 423 removed outlier: 3.572A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.625A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.520A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 488 through 512 removed outlier: 5.170A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.141A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.548A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 removed outlier: 3.518A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 47 removed outlier: 3.531A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.677A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.542A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 4.104A pdb=" N GLU D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.539A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.867A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.592A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.568A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 310 removed outlier: 3.786A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.556A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.073A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 404 Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 414 through 423 removed outlier: 3.573A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.624A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.520A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 488 through 512 removed outlier: 5.170A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.140A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.548A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 removed outlier: 3.518A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.731A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.482A 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: 6.732A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.481A 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: 6.731A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.481A 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: 6.732A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.481A 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 1077 hydrogen bonds defined for protein. 3111 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: 6.12 Time building geometry restraints manager: 8.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3256 1.31 - 1.43: 5696 1.43 - 1.56: 13146 1.56 - 1.69: 122 1.69 - 1.81: 272 Bond restraints: 22492 Sorted by residual: bond pdb=" C21 POV C 702 " pdb=" O21 POV C 702 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C21 POV B 702 " pdb=" O21 POV B 702 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C21 POV A 816 " pdb=" O21 POV A 816 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C21 POV D 706 " pdb=" O21 POV D 706 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV A 808 " pdb=" O21 POV A 808 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 1.99e+01 ... (remaining 22487 not shown) Histogram of bond angle deviations from ideal: 95.94 - 103.61: 338 103.61 - 111.27: 8808 111.27 - 118.94: 9605 118.94 - 126.61: 11104 126.61 - 134.27: 297 Bond angle restraints: 30152 Sorted by residual: angle pdb=" C ASN B 546 " pdb=" N TYR B 547 " pdb=" CA TYR B 547 " ideal model delta sigma weight residual 121.54 130.82 -9.28 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C ASN D 546 " pdb=" N TYR D 547 " pdb=" CA TYR D 547 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C ASN C 546 " pdb=" N TYR C 547 " pdb=" CA TYR C 547 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C ASN A 546 " pdb=" N TYR A 547 " pdb=" CA TYR A 547 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C12 POV D 706 " pdb=" N POV D 706 " pdb=" C14 POV D 706 " ideal model delta sigma weight residual 107.13 121.56 -14.43 3.00e+00 1.11e-01 2.31e+01 ... (remaining 30147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.74: 13464 30.74 - 61.47: 889 61.47 - 92.20: 103 92.20 - 122.94: 16 122.94 - 153.67: 16 Dihedral angle restraints: 14488 sinusoidal: 7304 harmonic: 7184 Sorted by residual: dihedral pdb=" CA GLU A 68 " pdb=" C GLU A 68 " pdb=" N ASP A 69 " pdb=" CA ASP A 69 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA GLU D 68 " pdb=" C GLU D 68 " pdb=" N ASP D 69 " pdb=" CA ASP D 69 " ideal model delta harmonic sigma weight residual 180.00 152.01 27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLU B 68 " pdb=" C GLU B 68 " pdb=" N ASP B 69 " pdb=" CA ASP B 69 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 14485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2936 0.092 - 0.185: 272 0.185 - 0.277: 11 0.277 - 0.369: 5 0.369 - 0.461: 8 Chirality restraints: 3232 Sorted by residual: chirality pdb=" CG LEU D 458 " pdb=" CB LEU D 458 " pdb=" CD1 LEU D 458 " pdb=" CD2 LEU D 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CG LEU A 458 " pdb=" CB LEU A 458 " pdb=" CD1 LEU A 458 " pdb=" CD2 LEU A 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CG LEU B 458 " pdb=" CB LEU B 458 " pdb=" CD1 LEU B 458 " pdb=" CD2 LEU B 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.25e+00 ... (remaining 3229 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 423 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO A 424 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 423 " 0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO C 424 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 424 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 424 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 423 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO B 424 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 424 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 424 " -0.041 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4472 2.77 - 3.30: 18784 3.30 - 3.83: 36279 3.83 - 4.37: 48614 4.37 - 4.90: 79694 Nonbonded interactions: 187843 Sorted by model distance: nonbonded pdb=" OG1 THR B 242 " pdb=" OE2 GLU B 282 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR D 242 " pdb=" OE2 GLU D 282 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR C 242 " pdb=" OE2 GLU C 282 " model vdw 2.235 2.440 nonbonded pdb=" OG1 THR A 242 " pdb=" OE2 GLU A 282 " model vdw 2.235 2.440 nonbonded pdb=" O HOH A 906 " pdb=" O HOH A 916 " model vdw 2.249 2.440 ... (remaining 187838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 637 or resid 806)) selection = (chain 'B' and (resid 24 through 637 or resid 706)) selection = (chain 'C' and (resid 24 through 637 or resid 706)) selection = (chain 'D' and (resid 24 through 637 or resid 706)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 1.120 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: 0.020 Extract box with map and model: 4.880 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 53.750 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.110 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.013 0.102 22492 Z= 0.775 Angle : 1.479 14.429 30152 Z= 0.649 Chirality : 0.059 0.461 3232 Planarity : 0.009 0.074 3600 Dihedral : 19.387 153.675 9848 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.31 % Allowed : 1.88 % Favored : 96.81 % Cbeta Deviations : 0.17 % 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: -4.89 (0.12), residues: 2448 helix: -3.72 (0.07), residues: 1492 sheet: -1.56 (0.51), residues: 88 loop : -2.08 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP D 629 HIS 0.014 0.003 HIS C 522 PHE 0.047 0.004 PHE B 472 TYR 0.023 0.004 TYR D 270 ARG 0.012 0.001 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 508 time to evaluate : 2.106 Fit side-chains REVERT: A 176 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6245 (mm-30) REVERT: A 234 LEU cc_start: 0.8562 (mp) cc_final: 0.8242 (mm) REVERT: A 239 GLN cc_start: 0.8634 (mt0) cc_final: 0.8332 (mt0) REVERT: A 263 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7669 (mtt90) REVERT: A 442 MET cc_start: 0.8859 (mtt) cc_final: 0.8659 (mtp) REVERT: A 458 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8579 (mt) REVERT: A 635 ASP cc_start: 0.7488 (t70) cc_final: 0.7181 (p0) REVERT: B 176 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6298 (mm-30) REVERT: B 234 LEU cc_start: 0.8593 (mp) cc_final: 0.8288 (mm) REVERT: B 239 GLN cc_start: 0.8649 (mt0) cc_final: 0.8348 (mt0) REVERT: B 263 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7515 (mtt90) REVERT: B 300 LYS cc_start: 0.8143 (mmtp) cc_final: 0.6977 (mppt) REVERT: B 383 ASP cc_start: 0.8071 (m-30) cc_final: 0.7858 (m-30) REVERT: B 635 ASP cc_start: 0.7393 (t70) cc_final: 0.7153 (p0) REVERT: C 176 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6270 (mm-30) REVERT: C 234 LEU cc_start: 0.8593 (mp) cc_final: 0.8290 (mm) REVERT: C 239 GLN cc_start: 0.8649 (mt0) cc_final: 0.8350 (mt0) REVERT: C 263 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7547 (mtt90) REVERT: C 442 MET cc_start: 0.8848 (mtt) cc_final: 0.8644 (mtp) REVERT: C 622 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6854 (pm20) REVERT: C 635 ASP cc_start: 0.7502 (t70) cc_final: 0.7170 (p0) REVERT: D 176 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6267 (mm-30) REVERT: D 234 LEU cc_start: 0.8619 (mp) cc_final: 0.8293 (mm) REVERT: D 239 GLN cc_start: 0.8646 (mt0) cc_final: 0.8349 (mt0) REVERT: D 263 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7647 (mtt90) REVERT: D 300 LYS cc_start: 0.8142 (mmtp) cc_final: 0.6930 (mppt) REVERT: D 442 MET cc_start: 0.8847 (mtt) cc_final: 0.8644 (mtp) REVERT: D 458 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8632 (mt) REVERT: D 635 ASP cc_start: 0.7446 (t70) cc_final: 0.7130 (p0) outliers start: 28 outliers final: 8 residues processed: 532 average time/residue: 1.3454 time to fit residues: 813.1191 Evaluate side-chains 347 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 337 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 122 HIS A 174 ASN A 185 HIS A 214 GLN A 369 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 122 HIS B 174 ASN B 185 HIS B 214 GLN B 306 GLN B 369 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN C 118 GLN C 122 HIS C 174 ASN C 185 HIS C 214 GLN C 369 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 122 HIS D 174 ASN D 185 HIS D 214 GLN D 369 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22492 Z= 0.283 Angle : 0.642 7.979 30152 Z= 0.317 Chirality : 0.042 0.279 3232 Planarity : 0.006 0.057 3600 Dihedral : 21.171 153.274 5100 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.67 % Allowed : 11.77 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2448 helix: -0.78 (0.12), residues: 1500 sheet: -1.08 (0.51), residues: 88 loop : -1.17 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 613 HIS 0.005 0.001 HIS D 522 PHE 0.016 0.002 PHE D 537 TYR 0.014 0.002 TYR C 432 ARG 0.004 0.001 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 363 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7616 (pt0) cc_final: 0.7346 (pm20) REVERT: A 157 CYS cc_start: 0.7996 (m) cc_final: 0.7731 (p) REVERT: A 176 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6136 (mm-30) REVERT: A 234 LEU cc_start: 0.8504 (mp) cc_final: 0.8246 (mm) REVERT: A 263 ARG cc_start: 0.8150 (mtt-85) cc_final: 0.7738 (mtt90) REVERT: A 300 LYS cc_start: 0.8081 (mmtp) cc_final: 0.6842 (mppt) REVERT: A 442 MET cc_start: 0.8603 (mtt) cc_final: 0.8389 (mtp) REVERT: A 618 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8093 (mp) REVERT: A 635 ASP cc_start: 0.7366 (t70) cc_final: 0.7131 (p0) REVERT: B 176 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6201 (mm-30) REVERT: B 234 LEU cc_start: 0.8535 (mp) cc_final: 0.8199 (mm) REVERT: B 263 ARG cc_start: 0.8121 (mtt-85) cc_final: 0.7680 (mtt90) REVERT: B 300 LYS cc_start: 0.8115 (mmtp) cc_final: 0.6960 (mppt) REVERT: B 618 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8237 (mp) REVERT: C 157 CYS cc_start: 0.8003 (m) cc_final: 0.7762 (p) REVERT: C 176 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6181 (mm-30) REVERT: C 234 LEU cc_start: 0.8559 (mp) cc_final: 0.8325 (mm) REVERT: C 263 ARG cc_start: 0.8161 (mtt-85) cc_final: 0.7742 (mtt90) REVERT: C 300 LYS cc_start: 0.8111 (mmtp) cc_final: 0.6920 (mppt) REVERT: C 442 MET cc_start: 0.8601 (mtt) cc_final: 0.8376 (mtp) REVERT: C 618 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8151 (mp) REVERT: C 635 ASP cc_start: 0.7338 (t70) cc_final: 0.7121 (p0) REVERT: D 80 GLU cc_start: 0.7619 (pt0) cc_final: 0.7402 (pm20) REVERT: D 157 CYS cc_start: 0.8011 (m) cc_final: 0.7761 (p) REVERT: D 176 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6219 (mm-30) REVERT: D 234 LEU cc_start: 0.8514 (mp) cc_final: 0.8266 (mm) REVERT: D 263 ARG cc_start: 0.8171 (mtt-85) cc_final: 0.7764 (mtt90) REVERT: D 300 LYS cc_start: 0.8105 (mmtp) cc_final: 0.6930 (mppt) REVERT: D 442 MET cc_start: 0.8605 (mtt) cc_final: 0.8379 (mtp) REVERT: D 615 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6979 (ttt180) REVERT: D 618 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8165 (mp) outliers start: 57 outliers final: 21 residues processed: 401 average time/residue: 1.2889 time to fit residues: 590.6883 Evaluate side-chains 354 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 328 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 615 ARG Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 178 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22492 Z= 0.326 Angle : 0.628 7.757 30152 Z= 0.311 Chirality : 0.042 0.207 3232 Planarity : 0.006 0.054 3600 Dihedral : 20.042 146.244 5096 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.13 % Allowed : 11.44 % Favored : 84.43 % 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: -0.21 (0.17), residues: 2448 helix: 0.48 (0.13), residues: 1504 sheet: -1.05 (0.51), residues: 88 loop : -1.04 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 613 HIS 0.005 0.001 HIS A 582 PHE 0.014 0.002 PHE B 537 TYR 0.013 0.002 TYR C 432 ARG 0.004 0.001 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 330 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6508 (tt0) REVERT: A 176 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6203 (mm-30) REVERT: A 214 GLN cc_start: 0.7591 (mt0) cc_final: 0.7345 (mt0) REVERT: A 234 LEU cc_start: 0.8582 (mp) cc_final: 0.8245 (mm) REVERT: A 263 ARG cc_start: 0.8223 (mtt-85) cc_final: 0.7737 (mtt90) REVERT: A 403 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: A 442 MET cc_start: 0.8573 (mtt) cc_final: 0.8327 (mtp) REVERT: A 589 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6967 (ttp80) REVERT: A 618 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8144 (mp) REVERT: A 628 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7799 (mtp180) REVERT: A 635 ASP cc_start: 0.7408 (t70) cc_final: 0.7177 (p0) REVERT: B 31 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6688 (tt0) REVERT: B 176 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6262 (mm-30) REVERT: B 214 GLN cc_start: 0.7629 (mt0) cc_final: 0.7391 (mt0) REVERT: B 234 LEU cc_start: 0.8593 (mp) cc_final: 0.8326 (mm) REVERT: B 263 ARG cc_start: 0.8223 (mtt-85) cc_final: 0.7765 (mtt90) REVERT: B 323 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7487 (mpt-90) REVERT: B 403 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: B 589 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7007 (ttp80) REVERT: B 618 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8296 (mp) REVERT: C 176 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6254 (mm-30) REVERT: C 214 GLN cc_start: 0.7636 (mt0) cc_final: 0.7403 (mt0) REVERT: C 234 LEU cc_start: 0.8597 (mp) cc_final: 0.8287 (mm) REVERT: C 263 ARG cc_start: 0.8242 (mtt-85) cc_final: 0.7792 (mtt90) REVERT: C 403 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: C 442 MET cc_start: 0.8576 (mtt) cc_final: 0.8328 (mtp) REVERT: C 589 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6972 (ttp80) REVERT: C 618 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8187 (mp) REVERT: C 628 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7844 (mtp180) REVERT: C 635 ASP cc_start: 0.7390 (t70) cc_final: 0.7182 (p0) REVERT: D 176 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6254 (mm-30) REVERT: D 234 LEU cc_start: 0.8610 (mp) cc_final: 0.8280 (mm) REVERT: D 263 ARG cc_start: 0.8241 (mtt-85) cc_final: 0.7966 (mtt90) REVERT: D 403 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: D 442 MET cc_start: 0.8585 (mtt) cc_final: 0.8337 (mtp) REVERT: D 589 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7013 (ttp80) REVERT: D 615 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7050 (ttt180) REVERT: D 618 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8211 (mp) outliers start: 88 outliers final: 43 residues processed: 376 average time/residue: 1.3536 time to fit residues: 578.1906 Evaluate side-chains 361 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 300 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 589 ARG Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 615 ARG Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.8980 chunk 166 optimal weight: 0.4980 chunk 115 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 chunk 222 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 211 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 369 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN B 73 HIS B 572 ASN C 73 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 73 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22492 Z= 0.136 Angle : 0.489 6.228 30152 Z= 0.246 Chirality : 0.037 0.164 3232 Planarity : 0.005 0.048 3600 Dihedral : 18.571 136.667 5096 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.72 % Allowed : 12.95 % Favored : 84.33 % 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 (0.17), residues: 2448 helix: 1.25 (0.14), residues: 1504 sheet: -1.08 (0.51), residues: 88 loop : -0.73 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 495 HIS 0.002 0.000 HIS A 265 PHE 0.010 0.001 PHE B 416 TYR 0.011 0.001 TYR A 524 ARG 0.004 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 312 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7576 (mtm110) cc_final: 0.6970 (mtp85) REVERT: A 176 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6280 (mm-30) REVERT: A 263 ARG cc_start: 0.8165 (mtt-85) cc_final: 0.7754 (mtt90) REVERT: A 314 LYS cc_start: 0.7786 (ttpt) cc_final: 0.7183 (ttmt) REVERT: A 442 MET cc_start: 0.8444 (mtt) cc_final: 0.8231 (mtp) REVERT: A 589 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7036 (ttp80) REVERT: A 628 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7715 (mtp180) REVERT: B 146 ARG cc_start: 0.7591 (mtm110) cc_final: 0.7003 (mtp85) REVERT: B 176 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6208 (mm-30) REVERT: B 263 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7786 (mtt90) REVERT: B 300 LYS cc_start: 0.8125 (mttm) cc_final: 0.6982 (mppt) REVERT: B 314 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7175 (ttmt) REVERT: B 323 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7539 (mpt-90) REVERT: B 589 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7035 (ttp80) REVERT: C 146 ARG cc_start: 0.7579 (mtm110) cc_final: 0.6994 (mtp85) REVERT: C 176 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6326 (mm-30) REVERT: C 263 ARG cc_start: 0.8194 (mtt-85) cc_final: 0.7819 (mtt90) REVERT: C 314 LYS cc_start: 0.7798 (ttpt) cc_final: 0.7190 (ttmt) REVERT: C 442 MET cc_start: 0.8445 (mtt) cc_final: 0.8234 (mtp) REVERT: C 589 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7039 (ttp80) REVERT: C 628 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7774 (mtp180) REVERT: D 146 ARG cc_start: 0.7583 (mtm110) cc_final: 0.6996 (mtp85) REVERT: D 176 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6322 (mm-30) REVERT: D 263 ARG cc_start: 0.8178 (mtt-85) cc_final: 0.7806 (mtt90) REVERT: D 300 LYS cc_start: 0.8123 (mmtm) cc_final: 0.6938 (mppt) REVERT: D 314 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7137 (ttmt) REVERT: D 442 MET cc_start: 0.8458 (mtt) cc_final: 0.8249 (mtp) REVERT: D 589 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7039 (ttp80) outliers start: 58 outliers final: 18 residues processed: 347 average time/residue: 1.3029 time to fit residues: 515.3285 Evaluate side-chains 326 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 299 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 589 ARG Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 589 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 120 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 369 GLN C 185 HIS C 369 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 369 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22492 Z= 0.246 Angle : 0.558 6.952 30152 Z= 0.276 Chirality : 0.040 0.195 3232 Planarity : 0.005 0.054 3600 Dihedral : 18.194 127.577 5096 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.81 % Allowed : 13.37 % Favored : 83.82 % 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: 0.83 (0.17), residues: 2448 helix: 1.40 (0.14), residues: 1500 sheet: -1.09 (0.51), residues: 88 loop : -0.72 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 613 HIS 0.003 0.001 HIS D 582 PHE 0.012 0.001 PHE B 537 TYR 0.012 0.002 TYR A 555 ARG 0.002 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 312 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6263 (mm-30) REVERT: A 263 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7809 (mtm-85) REVERT: A 314 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7170 (ttmt) REVERT: A 442 MET cc_start: 0.8525 (mtt) cc_final: 0.8290 (mtp) REVERT: A 589 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7017 (ttp80) REVERT: A 618 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8169 (mp) REVERT: A 628 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7747 (mtp180) REVERT: B 176 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6290 (mm-30) REVERT: B 263 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.7831 (mtt90) REVERT: B 314 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7187 (ttmt) REVERT: B 323 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7492 (mpt-90) REVERT: B 589 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.6988 (ttp80) REVERT: B 618 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8321 (mp) REVERT: C 146 ARG cc_start: 0.7628 (mtm110) cc_final: 0.7037 (mtp85) REVERT: C 176 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6313 (mm-30) REVERT: C 214 GLN cc_start: 0.7513 (mt0) cc_final: 0.7259 (mt0) REVERT: C 263 ARG cc_start: 0.8244 (mtt-85) cc_final: 0.7868 (mtm-85) REVERT: C 314 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7201 (ttmt) REVERT: C 442 MET cc_start: 0.8527 (mtt) cc_final: 0.8292 (mtp) REVERT: C 589 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6974 (ttp80) REVERT: C 618 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8231 (mp) REVERT: C 628 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7766 (mtp180) REVERT: D 176 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6263 (mm-30) REVERT: D 214 GLN cc_start: 0.7510 (mt0) cc_final: 0.7259 (mt0) REVERT: D 263 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.7846 (mtm-85) REVERT: D 314 LYS cc_start: 0.7793 (ttpt) cc_final: 0.7144 (ttmt) REVERT: D 442 MET cc_start: 0.8521 (mtt) cc_final: 0.8289 (mtp) REVERT: D 589 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7037 (ttp80) REVERT: D 618 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8227 (mp) outliers start: 60 outliers final: 31 residues processed: 344 average time/residue: 1.2898 time to fit residues: 506.9823 Evaluate side-chains 351 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 308 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 589 ARG Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 138 optimal weight: 0.0770 chunk 58 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 109 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 overall best weight: 0.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 290 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22492 Z= 0.142 Angle : 0.480 6.189 30152 Z= 0.241 Chirality : 0.037 0.180 3232 Planarity : 0.004 0.049 3600 Dihedral : 17.059 111.379 5096 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.25 % Allowed : 14.31 % Favored : 83.44 % 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: 1.15 (0.17), residues: 2448 helix: 1.68 (0.14), residues: 1508 sheet: -1.12 (0.52), residues: 88 loop : -0.67 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 495 HIS 0.002 0.000 HIS A 265 PHE 0.008 0.001 PHE B 537 TYR 0.010 0.001 TYR C 524 ARG 0.001 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 318 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7553 (mtm110) cc_final: 0.6997 (mtp85) REVERT: A 176 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6257 (mm-30) REVERT: A 263 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7796 (mtt90) REVERT: A 314 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7189 (ttmt) REVERT: A 442 MET cc_start: 0.8427 (mtt) cc_final: 0.8170 (mtp) REVERT: A 589 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7043 (ttp80) REVERT: A 628 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7687 (mtp180) REVERT: B 146 ARG cc_start: 0.7585 (mtm110) cc_final: 0.7047 (mtp85) REVERT: B 176 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6265 (mm-30) REVERT: B 263 ARG cc_start: 0.8183 (mtt-85) cc_final: 0.7791 (mtt90) REVERT: B 300 LYS cc_start: 0.8095 (mttm) cc_final: 0.6989 (mppt) REVERT: B 314 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7176 (ttmt) REVERT: B 323 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7528 (mpt-90) REVERT: B 578 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8293 (mtm) REVERT: B 589 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7025 (ttp80) REVERT: C 146 ARG cc_start: 0.7571 (mtm110) cc_final: 0.7038 (mtp85) REVERT: C 176 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6289 (mm-30) REVERT: C 263 ARG cc_start: 0.8239 (mtt-85) cc_final: 0.7868 (mtt90) REVERT: C 314 LYS cc_start: 0.7769 (ttpt) cc_final: 0.7177 (ttmt) REVERT: C 442 MET cc_start: 0.8430 (mtt) cc_final: 0.8178 (mtp) REVERT: C 589 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.6995 (ttp80) REVERT: C 628 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7717 (mtp180) REVERT: D 146 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7034 (mtp85) REVERT: D 176 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6269 (mm-30) REVERT: D 263 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7866 (mtt90) REVERT: D 314 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7179 (ttmt) REVERT: D 442 MET cc_start: 0.8442 (mtt) cc_final: 0.8220 (mtp) REVERT: D 589 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7030 (ttp80) outliers start: 48 outliers final: 27 residues processed: 337 average time/residue: 1.2734 time to fit residues: 492.1354 Evaluate side-chains 344 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 307 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 589 ARG Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 143 optimal weight: 0.0050 chunk 108 optimal weight: 4.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 369 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 369 GLN C 185 HIS C 369 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 369 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22492 Z= 0.179 Angle : 0.509 6.443 30152 Z= 0.254 Chirality : 0.038 0.182 3232 Planarity : 0.005 0.051 3600 Dihedral : 16.706 99.589 5096 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.39 % Allowed : 14.07 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.17), residues: 2448 helix: 1.76 (0.14), residues: 1500 sheet: -1.10 (0.52), residues: 88 loop : -0.57 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 583 HIS 0.002 0.001 HIS A 122 PHE 0.010 0.001 PHE D 553 TYR 0.011 0.001 TYR D 555 ARG 0.002 0.000 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 312 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7582 (mtm110) cc_final: 0.7051 (mtp85) REVERT: A 176 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6259 (mm-30) REVERT: A 263 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.7793 (mtt90) REVERT: A 314 LYS cc_start: 0.7772 (ttpt) cc_final: 0.7166 (ttmt) REVERT: A 442 MET cc_start: 0.8452 (mtt) cc_final: 0.8224 (mtp) REVERT: A 589 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6983 (ttp80) REVERT: A 628 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7714 (mtp180) REVERT: B 146 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7064 (mtp85) REVERT: B 176 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6332 (mm-30) REVERT: B 263 ARG cc_start: 0.8206 (mtt-85) cc_final: 0.7969 (mtt90) REVERT: B 314 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7145 (ttmt) REVERT: B 323 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7493 (mpt-90) REVERT: B 589 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.6999 (ttp80) REVERT: B 618 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 146 ARG cc_start: 0.7589 (mtm110) cc_final: 0.7079 (mtp85) REVERT: C 176 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6258 (mm-30) REVERT: C 263 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7870 (mtt90) REVERT: C 314 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7190 (ttmt) REVERT: C 442 MET cc_start: 0.8455 (mtt) cc_final: 0.8229 (mtp) REVERT: C 589 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6979 (ttp80) REVERT: C 628 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7728 (mtp180) REVERT: D 146 ARG cc_start: 0.7594 (mtm110) cc_final: 0.7081 (mtp85) REVERT: D 176 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6323 (mm-30) REVERT: D 263 ARG cc_start: 0.8229 (mtt-85) cc_final: 0.7861 (mtt90) REVERT: D 314 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7161 (ttmt) REVERT: D 442 MET cc_start: 0.8468 (mtt) cc_final: 0.8244 (mtp) REVERT: D 589 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7008 (ttp80) REVERT: D 618 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8259 (mp) outliers start: 51 outliers final: 30 residues processed: 332 average time/residue: 1.3038 time to fit residues: 495.4523 Evaluate side-chains 349 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 308 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 589 ARG Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22492 Z= 0.210 Angle : 0.530 6.630 30152 Z= 0.264 Chirality : 0.039 0.193 3232 Planarity : 0.005 0.048 3600 Dihedral : 16.563 92.511 5096 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.77 % Allowed : 13.93 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.17), residues: 2448 helix: 1.69 (0.14), residues: 1500 sheet: -1.05 (0.52), residues: 88 loop : -0.56 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 583 HIS 0.002 0.001 HIS B 122 PHE 0.010 0.001 PHE B 537 TYR 0.011 0.002 TYR A 555 ARG 0.002 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 321 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6272 (mm-30) REVERT: A 214 GLN cc_start: 0.7480 (mt0) cc_final: 0.7234 (mt0) REVERT: A 263 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7802 (mtt90) REVERT: A 314 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7167 (ttmt) REVERT: A 442 MET cc_start: 0.8460 (mtt) cc_final: 0.8197 (mtp) REVERT: A 589 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6993 (ttp80) REVERT: A 618 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8191 (mp) REVERT: A 628 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7732 (mtp180) REVERT: B 176 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6284 (mm-30) REVERT: B 263 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7808 (mtt90) REVERT: B 314 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7169 (ttmt) REVERT: B 323 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7487 (mpt-90) REVERT: B 589 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7006 (ttp80) REVERT: B 618 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8369 (mp) REVERT: C 146 ARG cc_start: 0.7592 (mtm110) cc_final: 0.7038 (mtp85) REVERT: C 176 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6311 (mm-30) REVERT: C 214 GLN cc_start: 0.7560 (mt0) cc_final: 0.7309 (mt0) REVERT: C 263 ARG cc_start: 0.8266 (mtt-85) cc_final: 0.7876 (mtt90) REVERT: C 314 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7195 (ttmt) REVERT: C 442 MET cc_start: 0.8464 (mtt) cc_final: 0.8198 (mtp) REVERT: C 589 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6982 (ttp80) REVERT: C 618 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8236 (mp) REVERT: C 628 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7741 (mtp180) REVERT: D 176 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6338 (mm-30) REVERT: D 214 GLN cc_start: 0.7493 (mt0) cc_final: 0.7240 (mt0) REVERT: D 263 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.7829 (mtt90) REVERT: D 314 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7152 (ttmt) REVERT: D 442 MET cc_start: 0.8479 (mtt) cc_final: 0.8213 (mtp) REVERT: D 589 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7014 (ttp80) REVERT: D 618 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8294 (mp) outliers start: 59 outliers final: 32 residues processed: 346 average time/residue: 1.3517 time to fit residues: 532.2105 Evaluate side-chains 360 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 315 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 589 ARG Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 chunk 219 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22492 Z= 0.191 Angle : 0.520 6.762 30152 Z= 0.259 Chirality : 0.039 0.187 3232 Planarity : 0.005 0.049 3600 Dihedral : 16.213 86.133 5096 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.91 % Allowed : 13.84 % Favored : 83.26 % 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: 1.28 (0.17), residues: 2448 helix: 1.76 (0.14), residues: 1500 sheet: -0.99 (0.53), residues: 88 loop : -0.53 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 583 HIS 0.002 0.001 HIS B 122 PHE 0.009 0.001 PHE C 537 TYR 0.010 0.001 TYR A 555 ARG 0.002 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 322 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6275 (mm-30) REVERT: A 263 ARG cc_start: 0.8216 (mtt-85) cc_final: 0.7792 (mtt90) REVERT: A 314 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7150 (ttmt) REVERT: A 442 MET cc_start: 0.8477 (mtt) cc_final: 0.8250 (mtp) REVERT: A 589 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7003 (ttp80) REVERT: A 618 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 628 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7689 (mtp180) REVERT: B 129 ASN cc_start: 0.8107 (t0) cc_final: 0.7859 (t160) REVERT: B 263 ARG cc_start: 0.8209 (mtt-85) cc_final: 0.7804 (mtt90) REVERT: B 314 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7156 (ttmt) REVERT: B 323 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7500 (mpt-90) REVERT: B 589 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7018 (ttp80) REVERT: B 618 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8287 (mp) REVERT: C 146 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7027 (mtp85) REVERT: C 177 GLU cc_start: 0.6927 (pm20) cc_final: 0.6448 (pt0) REVERT: C 263 ARG cc_start: 0.8257 (mtt-85) cc_final: 0.7872 (mtt90) REVERT: C 314 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7182 (ttmt) REVERT: C 442 MET cc_start: 0.8483 (mtt) cc_final: 0.8255 (mtp) REVERT: C 589 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6986 (ttp80) REVERT: C 618 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8232 (mp) REVERT: C 628 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7722 (mtp180) REVERT: D 176 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6331 (mm-30) REVERT: D 214 GLN cc_start: 0.7454 (mt0) cc_final: 0.7211 (mt0) REVERT: D 263 ARG cc_start: 0.8248 (mtt-85) cc_final: 0.7837 (mtt90) REVERT: D 314 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7143 (ttmt) REVERT: D 442 MET cc_start: 0.8498 (mtt) cc_final: 0.8270 (mtp) REVERT: D 589 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7014 (ttp80) REVERT: D 610 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7608 (tpm170) REVERT: D 618 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8257 (mp) outliers start: 62 outliers final: 32 residues processed: 352 average time/residue: 1.3209 time to fit residues: 529.6356 Evaluate side-chains 365 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 320 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 589 ARG Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 223 optimal weight: 0.0570 chunk 193 optimal weight: 5.9990 chunk 20 optimal weight: 0.0770 chunk 149 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22492 Z= 0.128 Angle : 0.479 6.468 30152 Z= 0.239 Chirality : 0.037 0.171 3232 Planarity : 0.004 0.049 3600 Dihedral : 15.421 80.327 5096 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.88 % Allowed : 15.24 % Favored : 82.88 % 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: 1.48 (0.18), residues: 2448 helix: 1.92 (0.14), residues: 1512 sheet: -0.98 (0.55), residues: 88 loop : -0.51 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 583 HIS 0.003 0.000 HIS D 185 PHE 0.007 0.001 PHE B 537 TYR 0.012 0.001 TYR B 524 ARG 0.002 0.000 ARG B 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 331 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7502 (mtm110) cc_final: 0.6957 (mtp85) REVERT: A 176 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6275 (mm-30) REVERT: A 177 GLU cc_start: 0.6843 (pm20) cc_final: 0.6324 (pt0) REVERT: A 263 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7715 (mtt90) REVERT: A 314 LYS cc_start: 0.7737 (ttpt) cc_final: 0.7150 (ttmt) REVERT: A 442 MET cc_start: 0.8382 (mtt) cc_final: 0.8143 (mtp) REVERT: A 589 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7018 (ttp80) REVERT: A 628 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7652 (mtp180) REVERT: B 130 MET cc_start: 0.7440 (tpt) cc_final: 0.7226 (tpt) REVERT: B 146 ARG cc_start: 0.7538 (mtm110) cc_final: 0.7001 (mtp85) REVERT: B 177 GLU cc_start: 0.6888 (pm20) cc_final: 0.6447 (pt0) REVERT: B 300 LYS cc_start: 0.8091 (mttm) cc_final: 0.6990 (mppt) REVERT: B 314 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7166 (ttmt) REVERT: B 589 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7766 (ttp-110) REVERT: C 146 ARG cc_start: 0.7510 (mtm110) cc_final: 0.6985 (mtp85) REVERT: C 177 GLU cc_start: 0.6936 (pm20) cc_final: 0.6459 (pt0) REVERT: C 263 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7802 (mtt90) REVERT: C 314 LYS cc_start: 0.7697 (ttpt) cc_final: 0.7159 (ttmt) REVERT: C 442 MET cc_start: 0.8385 (mtt) cc_final: 0.8150 (mtp) REVERT: C 589 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.6979 (ttp80) REVERT: C 628 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7684 (mtp180) REVERT: D 146 ARG cc_start: 0.7513 (mtm110) cc_final: 0.6987 (mtp85) REVERT: D 176 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6323 (mm-30) REVERT: D 177 GLU cc_start: 0.6944 (pm20) cc_final: 0.6479 (pt0) REVERT: D 263 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7976 (mtt90) REVERT: D 314 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7158 (ttmt) REVERT: D 442 MET cc_start: 0.8405 (mtt) cc_final: 0.8171 (mtp) REVERT: D 589 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7768 (ttp-110) outliers start: 40 outliers final: 24 residues processed: 350 average time/residue: 1.3281 time to fit residues: 530.8577 Evaluate side-chains 335 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 303 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 589 ARG Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 81 optimal weight: 0.0050 chunk 199 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 357 ASN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 357 ASN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 357 ASN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 357 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.178585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127181 restraints weight = 21611.807| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.57 r_work: 0.3367 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22492 Z= 0.147 Angle : 0.497 6.830 30152 Z= 0.247 Chirality : 0.037 0.174 3232 Planarity : 0.004 0.047 3600 Dihedral : 15.240 81.051 5096 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.74 % Allowed : 15.81 % Favored : 82.46 % 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: 1.62 (0.18), residues: 2448 helix: 2.01 (0.14), residues: 1504 sheet: -0.87 (0.55), residues: 88 loop : -0.37 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 583 HIS 0.004 0.001 HIS B 185 PHE 0.009 0.001 PHE A 537 TYR 0.011 0.001 TYR B 524 ARG 0.003 0.000 ARG B 323 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8589.59 seconds wall clock time: 152 minutes 6.67 seconds (9126.67 seconds total)