Starting phenix.real_space_refine on Sat Feb 17 17:31:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6n_25720/02_2024/7t6n_25720.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6n_25720/02_2024/7t6n_25720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6n_25720/02_2024/7t6n_25720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6n_25720/02_2024/7t6n_25720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6n_25720/02_2024/7t6n_25720.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6n_25720/02_2024/7t6n_25720.pdb" } resolution = 2.9 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= 0.007 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 55": "OE1" <-> "OE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 525": "OD1" <-> "OD2" Residue "B PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 525": "OD1" <-> "OD2" Residue "C PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 525": "OD1" <-> "OD2" Residue "D PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 10.75, per 1000 atoms: 0.55 Number of scatterers: 19412 At special positions: 0 Unit cell: (119.78, 119.78, 120.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.72 Conformation dependent library (CDL) restraints added in 3.6 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 8 sheets defined 68.9% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.754A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 removed outlier: 3.675A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 208 through 223 removed outlier: 3.984A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.790A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.305A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 410 Proline residue: A 405 - end of helix removed outlier: 3.570A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.691A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.979A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.621A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.902A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 608 removed outlier: 4.140A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.763A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 removed outlier: 3.677A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.534A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 208 through 223 removed outlier: 4.149A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.797A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.738A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.624A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.303A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 410 Proline residue: B 405 - end of helix removed outlier: 3.752A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.699A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 Processing helix chain 'B' and resid 488 through 512 removed outlier: 3.994A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.616A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.872A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 608 removed outlier: 4.077A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 608 " --> pdb=" O LEU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.752A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 removed outlier: 4.024A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.764A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 208 through 223 removed outlier: 4.030A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.791A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.741A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 306 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.304A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 410 Proline residue: C 405 - end of helix removed outlier: 3.682A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.700A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.971A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.629A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.865A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 608 removed outlier: 4.072A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 608 " --> pdb=" O LEU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.768A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 removed outlier: 3.661A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.566A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 206 Processing helix chain 'D' and resid 208 through 223 removed outlier: 4.019A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.799A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 304 through 310 Processing helix chain 'D' and resid 313 through 324 Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.304A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 410 Proline residue: D 405 - end of helix removed outlier: 3.688A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.691A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 Processing helix chain 'D' and resid 488 through 512 removed outlier: 3.988A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 512 " --> pdb=" O PHE D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.632A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.871A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 608 removed outlier: 4.074A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET D 608 " --> pdb=" O LEU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.634A pdb=" N LYS A 264 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP A 279 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (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: 6.625A pdb=" N LYS B 264 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP B 279 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (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: 6.629A pdb=" N LYS C 264 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP C 279 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (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: 6.631A pdb=" N LYS D 264 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP D 279 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1128 hydrogen bonds defined for protein. 3228 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: 6.25 Time building geometry restraints manager: 8.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5280 1.34 - 1.46: 4282 1.46 - 1.58: 10066 1.58 - 1.70: 4 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" CG PRO D 362 " pdb=" CD PRO D 362 " ideal model delta sigma weight residual 1.503 1.269 0.234 3.40e-02 8.65e+02 4.72e+01 bond pdb=" CG PRO B 362 " pdb=" CD PRO B 362 " ideal model delta sigma weight residual 1.503 1.269 0.234 3.40e-02 8.65e+02 4.72e+01 bond pdb=" CG PRO A 362 " pdb=" CD PRO A 362 " ideal model delta sigma weight residual 1.503 1.270 0.233 3.40e-02 8.65e+02 4.70e+01 bond pdb=" CG PRO C 362 " pdb=" CD PRO C 362 " ideal model delta sigma weight residual 1.503 1.271 0.232 3.40e-02 8.65e+02 4.67e+01 bond pdb=" CB PRO A 362 " pdb=" CG PRO A 362 " ideal model delta sigma weight residual 1.492 1.653 -0.161 5.00e-02 4.00e+02 1.03e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 89.45 - 98.38: 20 98.38 - 107.30: 736 107.30 - 116.23: 12117 116.23 - 125.15: 13699 125.15 - 134.07: 392 Bond angle restraints: 26964 Sorted by residual: angle pdb=" N PRO C 362 " pdb=" CD PRO C 362 " pdb=" CG PRO C 362 " ideal model delta sigma weight residual 103.20 89.45 13.75 1.50e+00 4.44e-01 8.40e+01 angle pdb=" N PRO D 362 " pdb=" CD PRO D 362 " pdb=" CG PRO D 362 " ideal model delta sigma weight residual 103.20 89.47 13.73 1.50e+00 4.44e-01 8.38e+01 angle pdb=" N PRO B 362 " pdb=" CD PRO B 362 " pdb=" CG PRO B 362 " ideal model delta sigma weight residual 103.20 89.47 13.73 1.50e+00 4.44e-01 8.38e+01 angle pdb=" N PRO A 362 " pdb=" CD PRO A 362 " pdb=" CG PRO A 362 " ideal model delta sigma weight residual 103.20 89.48 13.72 1.50e+00 4.44e-01 8.36e+01 angle pdb=" CA PRO B 362 " pdb=" N PRO B 362 " pdb=" CD PRO B 362 " ideal model delta sigma weight residual 112.00 99.48 12.52 1.40e+00 5.10e-01 8.00e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 10439 15.51 - 31.01: 1101 31.01 - 46.52: 184 46.52 - 62.03: 48 62.03 - 77.54: 40 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA MET D 485 " pdb=" C MET D 485 " pdb=" N ILE D 486 " pdb=" CA ILE D 486 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA MET B 485 " pdb=" C MET B 485 " pdb=" N ILE B 486 " pdb=" CA ILE B 486 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLN B 206 " pdb=" C GLN B 206 " pdb=" N PRO B 207 " pdb=" CA PRO B 207 " ideal model delta harmonic sigma weight residual 180.00 157.95 22.05 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2544 0.066 - 0.133: 423 0.133 - 0.199: 80 0.199 - 0.266: 8 0.266 - 0.332: 17 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB ILE A 429 " pdb=" CA ILE A 429 " pdb=" CG1 ILE A 429 " pdb=" CG2 ILE A 429 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE D 429 " pdb=" CA ILE D 429 " pdb=" CG1 ILE D 429 " pdb=" CG2 ILE D 429 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ASN B 208 " pdb=" N ASN B 208 " pdb=" C ASN B 208 " pdb=" CB ASN B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 361 " 0.109 5.00e-02 4.00e+02 1.54e-01 3.78e+01 pdb=" N PRO B 362 " -0.265 5.00e-02 4.00e+02 pdb=" CA PRO B 362 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO B 362 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 361 " -0.109 5.00e-02 4.00e+02 1.54e-01 3.77e+01 pdb=" N PRO C 362 " 0.265 5.00e-02 4.00e+02 pdb=" CA PRO C 362 " -0.081 5.00e-02 4.00e+02 pdb=" CD PRO C 362 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 361 " 0.109 5.00e-02 4.00e+02 1.53e-01 3.77e+01 pdb=" N PRO D 362 " -0.265 5.00e-02 4.00e+02 pdb=" CA PRO D 362 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO D 362 " 0.075 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6226 2.85 - 3.36: 17894 3.36 - 3.87: 33590 3.87 - 4.39: 38637 4.39 - 4.90: 66052 Nonbonded interactions: 162399 Sorted by model distance: nonbonded pdb=" OE1 GLU D 403 " pdb=" OH TYR D 415 " model vdw 2.335 2.440 nonbonded pdb=" OE1 GLU A 403 " pdb=" OH TYR A 415 " model vdw 2.340 2.440 nonbonded pdb=" OE1 GLU C 403 " pdb=" OH TYR C 415 " model vdw 2.340 2.440 nonbonded pdb=" OE1 GLU B 403 " pdb=" OH TYR B 415 " model vdw 2.356 2.440 nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.398 2.440 ... (remaining 162394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.770 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 52.660 Find NCS groups from input model: 1.180 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:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 : 0.007 0.234 19860 Z= 0.433 Angle : 1.076 13.745 26964 Z= 0.580 Chirality : 0.057 0.332 3072 Planarity : 0.010 0.154 3416 Dihedral : 13.709 77.537 7236 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.19 % Allowed : 0.33 % Favored : 99.48 % 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: -3.03 (0.14), residues: 2408 helix: -2.08 (0.10), residues: 1468 sheet: -2.19 (0.41), residues: 132 loop : -1.40 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 593 HIS 0.006 0.001 HIS B 201 PHE 0.062 0.003 PHE B 456 TYR 0.021 0.002 TYR A 339 ARG 0.016 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 363 time to evaluate : 2.199 Fit side-chains REVERT: A 323 LYS cc_start: 0.8394 (tppp) cc_final: 0.7995 (tppt) REVERT: A 429 ILE cc_start: 0.7665 (mt) cc_final: 0.7428 (mm) REVERT: A 447 MET cc_start: 0.7471 (ptm) cc_final: 0.7269 (ptt) REVERT: A 473 GLN cc_start: 0.8225 (tt0) cc_final: 0.8003 (tt0) REVERT: A 497 MET cc_start: 0.8330 (ttt) cc_final: 0.8106 (ttt) REVERT: B 93 GLU cc_start: 0.8268 (mp0) cc_final: 0.7977 (mp0) REVERT: B 473 GLN cc_start: 0.8229 (tt0) cc_final: 0.8002 (tt0) REVERT: C 323 LYS cc_start: 0.8393 (tppp) cc_final: 0.7982 (tppt) REVERT: C 399 ILE cc_start: 0.6899 (mt) cc_final: 0.6416 (mt) REVERT: C 429 ILE cc_start: 0.7532 (mt) cc_final: 0.7324 (mm) REVERT: C 473 GLN cc_start: 0.8235 (tt0) cc_final: 0.8011 (tt0) REVERT: D 93 GLU cc_start: 0.8272 (mp0) cc_final: 0.7973 (mp0) REVERT: D 177 GLU cc_start: 0.7435 (pm20) cc_final: 0.6799 (tp30) REVERT: D 323 LYS cc_start: 0.8369 (tppp) cc_final: 0.7964 (tppt) REVERT: D 399 ILE cc_start: 0.6876 (mt) cc_final: 0.6375 (mt) REVERT: D 429 ILE cc_start: 0.7586 (mt) cc_final: 0.7375 (mm) REVERT: D 447 MET cc_start: 0.7468 (ptm) cc_final: 0.7268 (ptt) REVERT: D 473 GLN cc_start: 0.8157 (tt0) cc_final: 0.7909 (tt0) outliers start: 4 outliers final: 0 residues processed: 367 average time/residue: 1.2990 time to fit residues: 534.9397 Evaluate side-chains 250 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 185 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN B 185 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN B 637 HIS C 74 GLN C 185 HIS ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN C 637 HIS D 74 GLN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19860 Z= 0.236 Angle : 0.597 7.114 26964 Z= 0.306 Chirality : 0.040 0.192 3072 Planarity : 0.005 0.040 3416 Dihedral : 4.101 17.192 2644 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.96 % Allowed : 9.40 % Favored : 88.65 % 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: -0.75 (0.16), residues: 2408 helix: -0.08 (0.12), residues: 1504 sheet: -2.22 (0.42), residues: 132 loop : -0.71 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 29 HIS 0.006 0.001 HIS C 84 PHE 0.026 0.002 PHE D 456 TYR 0.012 0.001 TYR B 559 ARG 0.008 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 283 time to evaluate : 2.318 Fit side-chains REVERT: A 80 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: A 93 GLU cc_start: 0.8264 (mp0) cc_final: 0.8039 (mp0) REVERT: A 323 LYS cc_start: 0.8259 (tppp) cc_final: 0.7872 (tppt) REVERT: A 473 GLN cc_start: 0.8200 (tt0) cc_final: 0.7980 (tt0) REVERT: A 615 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7766 (ttt180) REVERT: B 80 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7426 (pt0) REVERT: B 93 GLU cc_start: 0.8255 (mp0) cc_final: 0.8030 (mp0) REVERT: B 185 HIS cc_start: 0.7636 (m90) cc_final: 0.7424 (m-70) REVERT: B 473 GLN cc_start: 0.8214 (tt0) cc_final: 0.7989 (tt0) REVERT: B 615 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7754 (ttt180) REVERT: C 80 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7440 (pt0) REVERT: C 473 GLN cc_start: 0.8229 (tt0) cc_final: 0.8016 (tt0) REVERT: C 497 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8156 (ttt) REVERT: C 615 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7829 (ttt180) REVERT: D 80 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: D 177 GLU cc_start: 0.7509 (pm20) cc_final: 0.6741 (tp30) REVERT: D 615 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7786 (ttt180) outliers start: 41 outliers final: 5 residues processed: 302 average time/residue: 1.2904 time to fit residues: 439.0563 Evaluate side-chains 267 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 253 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 181 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 185 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 208 ASN D 67 ASN D 208 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19860 Z= 0.177 Angle : 0.536 6.667 26964 Z= 0.275 Chirality : 0.038 0.168 3072 Planarity : 0.004 0.036 3416 Dihedral : 3.809 16.181 2644 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.48 % Allowed : 11.35 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2408 helix: 0.93 (0.13), residues: 1504 sheet: -2.27 (0.42), residues: 132 loop : -0.47 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 593 HIS 0.004 0.001 HIS D 201 PHE 0.014 0.001 PHE B 487 TYR 0.007 0.001 TYR C 559 ARG 0.008 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 263 time to evaluate : 2.318 Fit side-chains REVERT: A 55 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6492 (mm-30) REVERT: A 177 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: A 399 ILE cc_start: 0.7310 (mt) cc_final: 0.6960 (mt) REVERT: A 447 MET cc_start: 0.7947 (ptm) cc_final: 0.7681 (ptp) REVERT: A 473 GLN cc_start: 0.8221 (tt0) cc_final: 0.8014 (tt0) REVERT: A 615 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7843 (ttt180) REVERT: B 55 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6598 (mm-30) REVERT: B 93 GLU cc_start: 0.8286 (mp0) cc_final: 0.8053 (mp0) REVERT: B 177 GLU cc_start: 0.7413 (pm20) cc_final: 0.7030 (tp30) REVERT: B 301 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7498 (mptm) REVERT: B 473 GLN cc_start: 0.8229 (tt0) cc_final: 0.7994 (tt0) REVERT: B 615 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7813 (ttt180) REVERT: C 55 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6596 (mm-30) REVERT: C 473 GLN cc_start: 0.8207 (tt0) cc_final: 0.7916 (tt0) REVERT: C 497 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8270 (ptm) REVERT: C 615 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7833 (ttt180) REVERT: D 55 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6487 (mm-30) REVERT: D 177 GLU cc_start: 0.7549 (pm20) cc_final: 0.6969 (tp30) REVERT: D 447 MET cc_start: 0.7942 (ptm) cc_final: 0.7664 (ptp) REVERT: D 615 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7824 (ttt180) outliers start: 31 outliers final: 14 residues processed: 280 average time/residue: 1.2537 time to fit residues: 396.5763 Evaluate side-chains 260 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 239 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN C 208 ASN D 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19860 Z= 0.227 Angle : 0.547 6.807 26964 Z= 0.281 Chirality : 0.039 0.200 3072 Planarity : 0.004 0.036 3416 Dihedral : 3.786 15.546 2644 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.77 % Allowed : 12.55 % Favored : 84.69 % 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: 0.86 (0.17), residues: 2408 helix: 1.32 (0.13), residues: 1504 sheet: -1.79 (0.48), residues: 112 loop : -0.41 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 593 HIS 0.005 0.001 HIS B 201 PHE 0.013 0.001 PHE C 425 TYR 0.011 0.001 TYR C 559 ARG 0.007 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 249 time to evaluate : 2.170 Fit side-chains REVERT: A 55 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6401 (mm-30) REVERT: A 93 GLU cc_start: 0.8291 (mp0) cc_final: 0.8057 (mp0) REVERT: A 108 GLU cc_start: 0.7205 (mp0) cc_final: 0.6683 (mp0) REVERT: A 177 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7197 (tp30) REVERT: A 447 MET cc_start: 0.7994 (ptm) cc_final: 0.7755 (ptp) REVERT: A 466 MET cc_start: 0.8659 (mtm) cc_final: 0.8365 (mtt) REVERT: A 473 GLN cc_start: 0.8235 (tt0) cc_final: 0.7969 (tt0) REVERT: A 615 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7866 (ttt180) REVERT: B 55 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6546 (mm-30) REVERT: B 80 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7514 (pt0) REVERT: B 93 GLU cc_start: 0.8290 (mp0) cc_final: 0.8045 (mp0) REVERT: B 177 GLU cc_start: 0.7428 (pm20) cc_final: 0.7075 (tp30) REVERT: B 301 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7447 (mptm) REVERT: B 473 GLN cc_start: 0.8232 (tt0) cc_final: 0.7990 (tt0) REVERT: B 497 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7883 (ttt) REVERT: B 615 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7841 (ttt180) REVERT: C 55 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6534 (mm-30) REVERT: C 177 GLU cc_start: 0.7424 (pm20) cc_final: 0.6823 (tp30) REVERT: C 473 GLN cc_start: 0.8243 (tt0) cc_final: 0.7979 (tt0) REVERT: C 482 ILE cc_start: 0.7752 (pt) cc_final: 0.7452 (mt) REVERT: C 497 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8234 (ttt) REVERT: C 615 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7857 (ttt180) REVERT: D 35 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6842 (ttt90) REVERT: D 55 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6458 (mm-30) REVERT: D 177 GLU cc_start: 0.7488 (pm20) cc_final: 0.6947 (tp30) REVERT: D 273 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7478 (pp) REVERT: D 447 MET cc_start: 0.7990 (ptm) cc_final: 0.7767 (ptp) REVERT: D 466 MET cc_start: 0.8590 (mtt) cc_final: 0.8216 (mtt) REVERT: D 497 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7923 (ttt) REVERT: D 615 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7849 (ttt180) outliers start: 58 outliers final: 8 residues processed: 285 average time/residue: 1.2394 time to fit residues: 399.8400 Evaluate side-chains 255 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 235 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 197 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.0070 chunk 208 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 208 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19860 Z= 0.138 Angle : 0.498 6.541 26964 Z= 0.255 Chirality : 0.038 0.173 3072 Planarity : 0.004 0.034 3416 Dihedral : 3.598 18.373 2644 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.72 % Allowed : 12.50 % Favored : 84.78 % 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: 1.31 (0.17), residues: 2408 helix: 1.75 (0.13), residues: 1504 sheet: -1.78 (0.48), residues: 112 loop : -0.36 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 593 HIS 0.002 0.000 HIS A 201 PHE 0.007 0.001 PHE D 537 TYR 0.005 0.001 TYR D 89 ARG 0.009 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 245 time to evaluate : 2.348 Fit side-chains REVERT: A 38 MET cc_start: 0.8667 (mmm) cc_final: 0.8403 (mmm) REVERT: A 55 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6333 (mm-30) REVERT: A 61 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.7036 (tp) REVERT: A 80 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7532 (pt0) REVERT: A 93 GLU cc_start: 0.8286 (mp0) cc_final: 0.8057 (mp0) REVERT: A 108 GLU cc_start: 0.7069 (mp0) cc_final: 0.6643 (mp0) REVERT: A 177 GLU cc_start: 0.7599 (pm20) cc_final: 0.7159 (tp30) REVERT: A 399 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.7040 (mt) REVERT: A 447 MET cc_start: 0.7876 (ptm) cc_final: 0.7640 (ptp) REVERT: A 466 MET cc_start: 0.8555 (mtm) cc_final: 0.8300 (mtt) REVERT: A 473 GLN cc_start: 0.8271 (tt0) cc_final: 0.8032 (tt0) REVERT: A 497 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7918 (ttm) REVERT: A 615 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7949 (ttm170) REVERT: B 43 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7388 (mmt90) REVERT: B 55 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6390 (mm-30) REVERT: B 80 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: B 93 GLU cc_start: 0.8281 (mp0) cc_final: 0.8038 (mp0) REVERT: B 108 GLU cc_start: 0.7064 (mp0) cc_final: 0.6628 (mp0) REVERT: B 177 GLU cc_start: 0.7508 (pm20) cc_final: 0.7162 (tp30) REVERT: B 301 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7481 (mptm) REVERT: B 399 ILE cc_start: 0.7484 (mt) cc_final: 0.7196 (mt) REVERT: B 486 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7794 (mt) REVERT: B 497 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7994 (ttm) REVERT: B 615 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7875 (ttm170) REVERT: C 55 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6393 (mm-30) REVERT: C 61 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7017 (tp) REVERT: C 80 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: C 177 GLU cc_start: 0.7394 (pm20) cc_final: 0.6931 (tp30) REVERT: C 184 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7412 (mt-10) REVERT: C 473 GLN cc_start: 0.8275 (tt0) cc_final: 0.8045 (tt0) REVERT: C 615 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7930 (ttm170) REVERT: D 35 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.6799 (ttt90) REVERT: D 55 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6330 (mm-30) REVERT: D 61 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7019 (tp) REVERT: D 80 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7506 (pt0) REVERT: D 108 GLU cc_start: 0.7052 (mp0) cc_final: 0.6629 (mp0) REVERT: D 177 GLU cc_start: 0.7437 (pm20) cc_final: 0.6985 (tp30) REVERT: D 447 MET cc_start: 0.7878 (ptm) cc_final: 0.7637 (ptp) REVERT: D 466 MET cc_start: 0.8473 (mtt) cc_final: 0.8151 (mtt) REVERT: D 486 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7909 (mt) REVERT: D 497 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7920 (ttm) REVERT: D 615 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7925 (ttm170) outliers start: 57 outliers final: 12 residues processed: 283 average time/residue: 1.2836 time to fit residues: 409.8179 Evaluate side-chains 265 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 233 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 7.9990 chunk 208 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 232 optimal weight: 0.5980 chunk 192 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS B 67 ASN B 637 HIS C 67 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS D 67 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19860 Z= 0.253 Angle : 0.568 7.121 26964 Z= 0.289 Chirality : 0.041 0.179 3072 Planarity : 0.004 0.040 3416 Dihedral : 3.801 16.899 2644 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.15 % Allowed : 14.41 % 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: 1.27 (0.17), residues: 2408 helix: 1.69 (0.13), residues: 1500 sheet: -1.13 (0.59), residues: 92 loop : -0.45 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 593 HIS 0.006 0.001 HIS B 201 PHE 0.014 0.002 PHE C 425 TYR 0.014 0.001 TYR A 559 ARG 0.009 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 225 time to evaluate : 2.219 Fit side-chains REVERT: A 55 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6490 (mm-30) REVERT: A 80 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7631 (pt0) REVERT: A 108 GLU cc_start: 0.7140 (mp0) cc_final: 0.6662 (mp0) REVERT: A 177 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7203 (tp30) REVERT: A 273 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7573 (pp) REVERT: A 615 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7853 (ttt180) REVERT: B 55 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6363 (mm-30) REVERT: B 177 GLU cc_start: 0.7515 (pm20) cc_final: 0.7048 (tp30) REVERT: B 273 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7567 (pp) REVERT: B 301 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7366 (mptm) REVERT: B 466 MET cc_start: 0.8583 (mtm) cc_final: 0.8210 (mtt) REVERT: B 486 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7978 (mt) REVERT: B 615 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7828 (ttt180) REVERT: C 55 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6682 (mm-30) REVERT: C 177 GLU cc_start: 0.7465 (pm20) cc_final: 0.6976 (tp30) REVERT: C 273 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7549 (pp) REVERT: C 473 GLN cc_start: 0.8281 (tt0) cc_final: 0.8053 (tt0) REVERT: C 615 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7849 (ttt180) REVERT: D 35 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6838 (ttt90) REVERT: D 55 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6603 (mm-30) REVERT: D 80 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7615 (pt0) REVERT: D 177 GLU cc_start: 0.7514 (pm20) cc_final: 0.7057 (tp30) REVERT: D 180 ARG cc_start: 0.7804 (mtt-85) cc_final: 0.7538 (mtt-85) REVERT: D 466 MET cc_start: 0.8642 (mtt) cc_final: 0.8400 (mtt) REVERT: D 486 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7997 (mt) REVERT: D 615 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7831 (ttt180) outliers start: 45 outliers final: 14 residues processed: 258 average time/residue: 1.2542 time to fit residues: 366.3175 Evaluate side-chains 241 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 213 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 231 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS C 67 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS D 67 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19860 Z= 0.200 Angle : 0.534 6.794 26964 Z= 0.274 Chirality : 0.039 0.172 3072 Planarity : 0.004 0.035 3416 Dihedral : 3.717 17.902 2644 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.34 % Allowed : 14.69 % Favored : 82.97 % 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: 1.31 (0.17), residues: 2408 helix: 1.80 (0.13), residues: 1500 sheet: -2.29 (0.45), residues: 132 loop : -0.31 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 593 HIS 0.004 0.001 HIS C 201 PHE 0.011 0.001 PHE C 425 TYR 0.009 0.001 TYR C 559 ARG 0.008 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 221 time to evaluate : 2.359 Fit side-chains REVERT: A 55 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6470 (mm-30) REVERT: A 80 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7623 (pt0) REVERT: A 93 GLU cc_start: 0.8291 (mp0) cc_final: 0.8061 (mp0) REVERT: A 108 GLU cc_start: 0.7134 (mp0) cc_final: 0.6679 (mp0) REVERT: A 177 GLU cc_start: 0.7535 (pm20) cc_final: 0.7177 (tp30) REVERT: A 273 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7576 (pp) REVERT: A 497 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7968 (ttt) REVERT: A 615 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7853 (ttt180) REVERT: B 93 GLU cc_start: 0.8277 (mp0) cc_final: 0.8046 (mp0) REVERT: B 177 GLU cc_start: 0.7471 (pm20) cc_final: 0.7134 (tp30) REVERT: B 273 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7575 (pp) REVERT: B 301 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7365 (mptm) REVERT: B 466 MET cc_start: 0.8575 (mtm) cc_final: 0.8247 (mtt) REVERT: B 486 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7972 (mt) REVERT: B 497 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7940 (ttm) REVERT: B 615 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7795 (ttt180) REVERT: C 55 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6542 (mm-30) REVERT: C 177 GLU cc_start: 0.7476 (pm20) cc_final: 0.7024 (tp30) REVERT: C 184 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7538 (mt-10) REVERT: C 273 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7584 (pp) REVERT: C 466 MET cc_start: 0.8486 (mtm) cc_final: 0.8070 (mtt) REVERT: C 473 GLN cc_start: 0.8268 (tt0) cc_final: 0.8054 (tt0) REVERT: C 615 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7846 (ttt180) REVERT: D 35 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6857 (ttt90) REVERT: D 55 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6433 (mm-30) REVERT: D 80 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7602 (pt0) REVERT: D 177 GLU cc_start: 0.7487 (pm20) cc_final: 0.7113 (tp30) REVERT: D 180 ARG cc_start: 0.7896 (mtt-85) cc_final: 0.7575 (mtt-85) REVERT: D 184 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7405 (mt-10) REVERT: D 273 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7532 (pp) REVERT: D 466 MET cc_start: 0.8571 (mtt) cc_final: 0.8305 (mtt) REVERT: D 615 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7840 (ttt180) outliers start: 49 outliers final: 15 residues processed: 257 average time/residue: 1.2325 time to fit residues: 358.9511 Evaluate side-chains 245 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 215 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS D 128 GLN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19860 Z= 0.273 Angle : 0.579 7.127 26964 Z= 0.296 Chirality : 0.041 0.179 3072 Planarity : 0.004 0.035 3416 Dihedral : 3.858 17.387 2644 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.29 % Allowed : 14.65 % Favored : 83.06 % 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: 1.22 (0.17), residues: 2408 helix: 1.66 (0.13), residues: 1500 sheet: -1.19 (0.60), residues: 92 loop : -0.49 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 593 HIS 0.006 0.001 HIS B 201 PHE 0.015 0.002 PHE A 425 TYR 0.012 0.001 TYR D 559 ARG 0.007 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 2.299 Fit side-chains REVERT: A 80 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7704 (pt0) REVERT: A 177 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: A 273 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7538 (pp) REVERT: A 615 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7853 (ttt180) REVERT: B 177 GLU cc_start: 0.7473 (pm20) cc_final: 0.7066 (tp30) REVERT: B 273 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7530 (pp) REVERT: B 301 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7339 (mptm) REVERT: B 486 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8050 (mt) REVERT: B 615 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7867 (ttt180) REVERT: C 177 GLU cc_start: 0.7534 (pm20) cc_final: 0.7111 (tp30) REVERT: C 273 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7541 (pp) REVERT: C 466 MET cc_start: 0.8602 (mtm) cc_final: 0.8222 (mtt) REVERT: C 473 GLN cc_start: 0.8213 (tt0) cc_final: 0.8007 (tt0) REVERT: C 474 MET cc_start: 0.7527 (ptm) cc_final: 0.7113 (ptm) REVERT: C 615 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7906 (ttt180) REVERT: D 35 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6856 (ttt90) REVERT: D 80 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: D 177 GLU cc_start: 0.7461 (pm20) cc_final: 0.7104 (tp30) REVERT: D 273 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7461 (pp) REVERT: D 615 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7837 (ttt180) outliers start: 48 outliers final: 21 residues processed: 247 average time/residue: 1.3246 time to fit residues: 369.1909 Evaluate side-chains 240 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 205 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 286 TRP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.7980 chunk 221 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS B 67 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS C 67 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS D 67 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19860 Z= 0.187 Angle : 0.531 6.798 26964 Z= 0.272 Chirality : 0.039 0.169 3072 Planarity : 0.004 0.035 3416 Dihedral : 3.721 19.611 2644 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.00 % Allowed : 15.22 % Favored : 82.78 % 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 (0.17), residues: 2408 helix: 1.86 (0.13), residues: 1500 sheet: -0.30 (0.68), residues: 72 loop : -0.50 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 29 HIS 0.004 0.001 HIS C 201 PHE 0.011 0.001 PHE C 456 TYR 0.008 0.001 TYR A 559 ARG 0.007 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 211 time to evaluate : 2.223 Fit side-chains REVERT: A 38 MET cc_start: 0.8654 (mmm) cc_final: 0.8430 (mmm) REVERT: A 80 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7622 (pt0) REVERT: A 93 GLU cc_start: 0.8299 (mp0) cc_final: 0.8061 (mp0) REVERT: A 177 GLU cc_start: 0.7549 (pm20) cc_final: 0.7168 (tp30) REVERT: A 273 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7526 (pp) REVERT: A 486 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8079 (mt) REVERT: A 615 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7844 (ttt180) REVERT: B 80 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7493 (pt0) REVERT: B 93 GLU cc_start: 0.8287 (mp0) cc_final: 0.8057 (mp0) REVERT: B 177 GLU cc_start: 0.7443 (pm20) cc_final: 0.7112 (tp30) REVERT: B 273 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7550 (pp) REVERT: B 301 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7354 (mptm) REVERT: B 466 MET cc_start: 0.8543 (mtt) cc_final: 0.8194 (mtt) REVERT: B 486 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7956 (mt) REVERT: B 615 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7791 (ttt180) REVERT: C 80 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: C 177 GLU cc_start: 0.7506 (pm20) cc_final: 0.7036 (tp30) REVERT: C 273 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7531 (pp) REVERT: C 466 MET cc_start: 0.8488 (mtm) cc_final: 0.8148 (mtt) REVERT: C 473 GLN cc_start: 0.8250 (tt0) cc_final: 0.8023 (tt0) REVERT: C 615 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7806 (ttt180) REVERT: D 35 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6771 (ttt90) REVERT: D 80 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7604 (pt0) REVERT: D 177 GLU cc_start: 0.7464 (pm20) cc_final: 0.7091 (tp30) REVERT: D 273 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7493 (pp) REVERT: D 615 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7788 (ttt180) outliers start: 42 outliers final: 16 residues processed: 241 average time/residue: 1.3330 time to fit residues: 361.6017 Evaluate side-chains 242 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 210 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 0.0370 chunk 158 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS B 67 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS C 67 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS D 67 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19860 Z= 0.241 Angle : 0.562 6.965 26964 Z= 0.287 Chirality : 0.040 0.173 3072 Planarity : 0.004 0.035 3416 Dihedral : 3.805 20.842 2644 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.67 % Allowed : 16.08 % Favored : 82.25 % 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: 1.35 (0.17), residues: 2408 helix: 1.75 (0.13), residues: 1500 sheet: -0.32 (0.69), residues: 72 loop : -0.53 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 29 HIS 0.005 0.001 HIS D 201 PHE 0.013 0.001 PHE C 456 TYR 0.011 0.001 TYR C 559 ARG 0.005 0.000 ARG D 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 212 time to evaluate : 2.361 Fit side-chains REVERT: A 80 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7634 (pt0) REVERT: A 93 GLU cc_start: 0.8301 (mp0) cc_final: 0.8078 (mp0) REVERT: A 177 GLU cc_start: 0.7555 (pm20) cc_final: 0.7166 (tp30) REVERT: A 273 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7535 (pp) REVERT: A 466 MET cc_start: 0.8560 (mtm) cc_final: 0.8109 (mtt) REVERT: A 474 MET cc_start: 0.7505 (ptm) cc_final: 0.7084 (ptt) REVERT: A 486 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8074 (mt) REVERT: A 615 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7869 (ttt180) REVERT: B 80 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: B 93 GLU cc_start: 0.8289 (mp0) cc_final: 0.8009 (mp0) REVERT: B 177 GLU cc_start: 0.7445 (pm20) cc_final: 0.7062 (tp30) REVERT: B 273 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7528 (pp) REVERT: B 301 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7360 (mptm) REVERT: B 466 MET cc_start: 0.8551 (mtt) cc_final: 0.8194 (mtt) REVERT: B 486 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.8020 (mt) REVERT: B 615 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7841 (ttt180) REVERT: C 177 GLU cc_start: 0.7530 (pm20) cc_final: 0.7077 (tp30) REVERT: C 273 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7540 (pp) REVERT: C 466 MET cc_start: 0.8579 (mtm) cc_final: 0.8234 (mtt) REVERT: C 615 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7826 (ttt180) REVERT: D 35 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.6836 (ttt90) REVERT: D 80 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7631 (pt0) REVERT: D 177 GLU cc_start: 0.7447 (pm20) cc_final: 0.7086 (tp30) REVERT: D 466 MET cc_start: 0.8531 (mtm) cc_final: 0.8181 (mtt) REVERT: D 615 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7806 (ttt180) outliers start: 35 outliers final: 17 residues processed: 234 average time/residue: 1.4082 time to fit residues: 369.1349 Evaluate side-chains 240 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 209 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106108 restraints weight = 22806.477| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.57 r_work: 0.3244 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19860 Z= 0.194 Angle : 0.539 6.868 26964 Z= 0.276 Chirality : 0.039 0.171 3072 Planarity : 0.004 0.035 3416 Dihedral : 3.749 22.158 2644 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.72 % Allowed : 16.36 % Favored : 81.92 % 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 (0.17), residues: 2408 helix: 1.86 (0.13), residues: 1500 sheet: -0.37 (0.68), residues: 72 loop : -0.49 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 29 HIS 0.004 0.001 HIS D 201 PHE 0.015 0.001 PHE C 456 TYR 0.008 0.001 TYR C 559 ARG 0.007 0.000 ARG A 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6607.75 seconds wall clock time: 118 minutes 39.50 seconds (7119.50 seconds total)