Starting phenix.real_space_refine on Sun Mar 17 23:07:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zje_14746/03_2024/7zje_14746.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zje_14746/03_2024/7zje_14746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zje_14746/03_2024/7zje_14746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zje_14746/03_2024/7zje_14746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zje_14746/03_2024/7zje_14746.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zje_14746/03_2024/7zje_14746.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 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 112 5.16 5 C 12656 2.51 5 N 3224 2.21 5 O 3292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 145": "OD1" <-> "OD2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 647": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19284 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4821 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4821 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4821 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4821 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 9.98, per 1000 atoms: 0.52 Number of scatterers: 19284 At special positions: 0 Unit cell: (148.12, 148.12, 115.957, 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 112 16.00 O 3292 8.00 N 3224 7.00 C 12656 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: 7.61 Conformation dependent library (CDL) restraints added in 3.9 seconds 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 66.6% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 76 through 82 removed outlier: 4.164A pdb=" N PHE A 81 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.605A pdb=" N THR A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.958A pdb=" N ASP A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.822A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.712A pdb=" N GLN A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.694A pdb=" N ALA A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.549A pdb=" N MET A 372 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.766A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 414 Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.608A pdb=" N SER A 466 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.581A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.689A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.700A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 537 removed outlier: 4.283A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.883A pdb=" N PHE A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 648 removed outlier: 3.880A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.766A pdb=" N ASN A 655 " --> pdb=" O HIS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 673 removed outlier: 3.596A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.721A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 82 removed outlier: 4.164A pdb=" N PHE B 81 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.606A pdb=" N THR B 93 " --> pdb=" O PRO B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.958A pdb=" N ASP B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.822A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 196 through 204 removed outlier: 3.712A pdb=" N GLN B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS B 202 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.694A pdb=" N ALA B 265 " --> pdb=" O PRO B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.549A pdb=" N MET B 372 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 389 removed outlier: 3.766A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 414 Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.609A pdb=" N SER B 466 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.583A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.689A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 removed outlier: 3.701A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 537 removed outlier: 4.284A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 597 through 606 removed outlier: 3.884A pdb=" N PHE B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 648 removed outlier: 3.879A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.767A pdb=" N ASN B 655 " --> pdb=" O HIS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 673 removed outlier: 3.596A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 removed outlier: 3.721A pdb=" N THR B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 removed outlier: 4.164A pdb=" N PHE C 81 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 removed outlier: 3.606A pdb=" N THR C 93 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.958A pdb=" N ASP C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.822A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 196 through 204 removed outlier: 3.711A pdb=" N GLN C 200 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.693A pdb=" N ALA C 265 " --> pdb=" O PRO C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 308 through 316 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.548A pdb=" N MET C 372 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 389 removed outlier: 3.766A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 414 Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 460 through 466 removed outlier: 3.608A pdb=" N SER C 466 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.582A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET C 492 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.689A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 removed outlier: 3.700A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 537 removed outlier: 4.284A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 Processing helix chain 'C' and resid 597 through 606 removed outlier: 3.883A pdb=" N PHE C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 648 removed outlier: 3.879A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 656 removed outlier: 3.767A pdb=" N ASN C 655 " --> pdb=" O HIS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 673 removed outlier: 3.596A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 removed outlier: 3.721A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 82 removed outlier: 4.164A pdb=" N PHE D 81 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 removed outlier: 3.606A pdb=" N THR D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.958A pdb=" N ASP D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.822A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.712A pdb=" N GLN D 200 " --> pdb=" O GLY D 196 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS D 202 " --> pdb=" O PHE D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.693A pdb=" N ALA D 265 " --> pdb=" O PRO D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.549A pdb=" N MET D 372 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 389 removed outlier: 3.766A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 414 Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.609A pdb=" N SER D 466 " --> pdb=" O ILE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.582A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 511 removed outlier: 3.689A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 518 removed outlier: 3.701A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 537 removed outlier: 4.284A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 Processing helix chain 'D' and resid 597 through 606 removed outlier: 3.884A pdb=" N PHE D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 648 removed outlier: 3.880A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 656 removed outlier: 3.767A pdb=" N ASN D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 673 removed outlier: 3.596A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 removed outlier: 3.721A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 332 Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 332 Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 332 Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 332 1036 hydrogen bonds defined for protein. 2976 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: 5.31 Time building geometry restraints manager: 8.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5996 1.35 - 1.46: 4844 1.46 - 1.58: 8748 1.58 - 1.70: 0 1.70 - 1.81: 172 Bond restraints: 19760 Sorted by residual: bond pdb=" N MET A 640 " pdb=" CA MET A 640 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.65e+00 bond pdb=" N MET D 640 " pdb=" CA MET D 640 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.59e+00 bond pdb=" N MET C 640 " pdb=" CA MET C 640 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.19e-02 7.06e+03 4.03e+00 bond pdb=" N MET B 640 " pdb=" CA MET B 640 " ideal model delta sigma weight residual 1.459 1.483 -0.023 1.19e-02 7.06e+03 3.89e+00 bond pdb=" C GLU A 376 " pdb=" N PRO A 377 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.37e+00 ... (remaining 19755 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.83: 463 106.83 - 113.62: 10877 113.62 - 120.42: 7680 120.42 - 127.21: 7531 127.21 - 134.01: 253 Bond angle restraints: 26804 Sorted by residual: angle pdb=" CA GLU D 352 " pdb=" CB GLU D 352 " pdb=" CG GLU D 352 " ideal model delta sigma weight residual 114.10 120.51 -6.41 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA GLU C 352 " pdb=" CB GLU C 352 " pdb=" CG GLU C 352 " ideal model delta sigma weight residual 114.10 120.49 -6.39 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA GLU B 352 " pdb=" CB GLU B 352 " pdb=" CG GLU B 352 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA GLU A 352 " pdb=" CB GLU A 352 " pdb=" CG GLU A 352 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C PHE D 519 " pdb=" N GLN D 520 " pdb=" CA GLN D 520 " ideal model delta sigma weight residual 120.82 124.97 -4.15 1.50e+00 4.44e-01 7.66e+00 ... (remaining 26799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 10459 14.15 - 28.30: 731 28.30 - 42.45: 334 42.45 - 56.60: 44 56.60 - 70.74: 8 Dihedral angle restraints: 11576 sinusoidal: 4620 harmonic: 6956 Sorted by residual: dihedral pdb=" CA LEU A 345 " pdb=" C LEU A 345 " pdb=" N SER A 346 " pdb=" CA SER A 346 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LEU B 345 " pdb=" C LEU B 345 " pdb=" N SER B 346 " pdb=" CA SER B 346 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LEU D 345 " pdb=" C LEU D 345 " pdb=" N SER D 346 " pdb=" CA SER D 346 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 11573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2070 0.033 - 0.066: 750 0.066 - 0.100: 192 0.100 - 0.133: 24 0.133 - 0.166: 8 Chirality restraints: 3044 Sorted by residual: chirality pdb=" CA MET A 640 " pdb=" N MET A 640 " pdb=" C MET A 640 " pdb=" CB MET A 640 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA MET C 640 " pdb=" N MET C 640 " pdb=" C MET C 640 " pdb=" CB MET C 640 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA MET B 640 " pdb=" N MET B 640 " pdb=" C MET B 640 " pdb=" CB MET B 640 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 3041 not shown) Planarity restraints: 3292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 148 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO B 149 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 149 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 149 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 148 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO C 149 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 148 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO D 149 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.027 5.00e-02 4.00e+02 ... (remaining 3289 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4228 2.78 - 3.31: 19254 3.31 - 3.84: 30476 3.84 - 4.37: 33303 4.37 - 4.90: 59116 Nonbonded interactions: 146377 Sorted by model distance: nonbonded pdb=" O PRO A 89 " pdb=" OG1 THR A 93 " model vdw 2.254 2.440 nonbonded pdb=" O PRO D 89 " pdb=" OG1 THR D 93 " model vdw 2.255 2.440 nonbonded pdb=" O PRO C 89 " pdb=" OG1 THR C 93 " model vdw 2.255 2.440 nonbonded pdb=" O PRO B 89 " pdb=" OG1 THR B 93 " model vdw 2.255 2.440 nonbonded pdb=" OD1 ASP C 258 " pdb=" ND2 ASN C 263 " model vdw 2.292 2.520 ... (remaining 146372 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.690 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 49.730 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.002 0.038 19760 Z= 0.157 Angle : 0.574 6.455 26804 Z= 0.300 Chirality : 0.037 0.166 3044 Planarity : 0.004 0.049 3292 Dihedral : 11.987 70.744 7080 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.35 % Favored : 91.14 % Rotamer: Outliers : 0.19 % Allowed : 0.24 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2348 helix: 1.55 (0.14), residues: 1456 sheet: 2.42 (0.56), residues: 80 loop : -1.98 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 223 HIS 0.005 0.001 HIS C 165 PHE 0.014 0.001 PHE A 407 TYR 0.010 0.001 TYR A 271 ARG 0.003 0.000 ARG C 679 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 308 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 ASP cc_start: 0.8653 (t70) cc_final: 0.8043 (t0) REVERT: B 536 ASP cc_start: 0.8661 (t70) cc_final: 0.8030 (t0) REVERT: C 536 ASP cc_start: 0.8685 (t70) cc_final: 0.8053 (t0) REVERT: D 536 ASP cc_start: 0.8702 (t70) cc_final: 0.8242 (t0) outliers start: 4 outliers final: 0 residues processed: 308 average time/residue: 0.2623 time to fit residues: 129.0828 Evaluate side-chains 262 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.5980 chunk 178 optimal weight: 0.0030 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 120 optimal weight: 0.0570 chunk 95 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 overall best weight: 0.5310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19760 Z= 0.142 Angle : 0.543 9.289 26804 Z= 0.265 Chirality : 0.036 0.131 3044 Planarity : 0.004 0.044 3292 Dihedral : 3.580 17.281 2588 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.24 % Favored : 92.25 % Rotamer: Outliers : 0.62 % Allowed : 7.26 % Favored : 92.12 % 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: 1.12 (0.19), residues: 2348 helix: 1.84 (0.14), residues: 1440 sheet: 2.43 (0.57), residues: 80 loop : -1.50 (0.24), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 386 HIS 0.003 0.001 HIS C 165 PHE 0.011 0.001 PHE D 407 TYR 0.022 0.001 TYR C 471 ARG 0.002 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 281 time to evaluate : 2.160 Fit side-chains REVERT: A 349 ASP cc_start: 0.7728 (t0) cc_final: 0.7396 (t0) REVERT: A 521 HIS cc_start: 0.8011 (m-70) cc_final: 0.7650 (p-80) REVERT: A 536 ASP cc_start: 0.8487 (t70) cc_final: 0.8150 (t0) REVERT: A 672 GLU cc_start: 0.8589 (tt0) cc_final: 0.8363 (tt0) REVERT: B 471 TYR cc_start: 0.7498 (p90) cc_final: 0.7269 (p90) REVERT: B 521 HIS cc_start: 0.7912 (m-70) cc_final: 0.7467 (p-80) REVERT: B 536 ASP cc_start: 0.8482 (t70) cc_final: 0.8239 (t0) REVERT: C 536 ASP cc_start: 0.8487 (t70) cc_final: 0.8240 (t0) REVERT: D 536 ASP cc_start: 0.8532 (t70) cc_final: 0.8158 (t0) outliers start: 13 outliers final: 5 residues processed: 286 average time/residue: 0.2749 time to fit residues: 124.0897 Evaluate side-chains 274 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 269 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 153 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 50.0000 chunk 66 optimal weight: 0.3980 chunk 178 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS D 165 HIS D 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19760 Z= 0.216 Angle : 0.577 8.653 26804 Z= 0.283 Chirality : 0.038 0.168 3044 Planarity : 0.004 0.045 3292 Dihedral : 3.728 20.439 2588 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.22 % Favored : 91.27 % Rotamer: Outliers : 0.91 % Allowed : 10.96 % Favored : 88.12 % 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: 1.00 (0.19), residues: 2348 helix: 1.73 (0.14), residues: 1420 sheet: 2.36 (0.55), residues: 80 loop : -1.43 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 223 HIS 0.004 0.001 HIS B 251 PHE 0.016 0.001 PHE C 407 TYR 0.021 0.001 TYR C 471 ARG 0.002 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 288 time to evaluate : 2.145 Fit side-chains REVERT: A 521 HIS cc_start: 0.8032 (m-70) cc_final: 0.7637 (p-80) REVERT: A 645 MET cc_start: 0.8385 (mmm) cc_final: 0.8081 (tpt) REVERT: A 672 GLU cc_start: 0.8550 (tt0) cc_final: 0.8285 (tt0) REVERT: B 471 TYR cc_start: 0.7567 (p90) cc_final: 0.7363 (p90) REVERT: B 521 HIS cc_start: 0.7925 (m-70) cc_final: 0.7437 (p-80) REVERT: B 536 ASP cc_start: 0.8488 (t70) cc_final: 0.8257 (t0) REVERT: B 640 MET cc_start: 0.8789 (tmm) cc_final: 0.8457 (mmp) REVERT: B 672 GLU cc_start: 0.8589 (tt0) cc_final: 0.8304 (tt0) REVERT: C 471 TYR cc_start: 0.7569 (p90) cc_final: 0.7368 (p90) REVERT: C 521 HIS cc_start: 0.7902 (m-70) cc_final: 0.7330 (p-80) REVERT: C 536 ASP cc_start: 0.8505 (t70) cc_final: 0.8288 (t0) REVERT: C 640 MET cc_start: 0.8754 (tmm) cc_final: 0.8428 (mmp) REVERT: D 471 TYR cc_start: 0.7570 (p90) cc_final: 0.7362 (p90) REVERT: D 521 HIS cc_start: 0.7942 (m-70) cc_final: 0.7362 (p-80) REVERT: D 536 ASP cc_start: 0.8495 (t70) cc_final: 0.8178 (t0) REVERT: D 640 MET cc_start: 0.8786 (tmm) cc_final: 0.8482 (mmp) outliers start: 19 outliers final: 8 residues processed: 296 average time/residue: 0.3035 time to fit residues: 136.2739 Evaluate side-chains 282 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 274 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 0.3980 chunk 215 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 112 optimal weight: 0.0070 chunk 204 optimal weight: 3.9990 chunk 61 optimal weight: 30.0000 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19760 Z= 0.143 Angle : 0.537 8.843 26804 Z= 0.262 Chirality : 0.036 0.141 3044 Planarity : 0.003 0.046 3292 Dihedral : 3.660 18.590 2588 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.37 % Favored : 92.12 % Rotamer: Outliers : 0.82 % Allowed : 12.45 % Favored : 86.73 % 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: 1.14 (0.19), residues: 2348 helix: 1.89 (0.14), residues: 1420 sheet: 1.86 (0.55), residues: 88 loop : -1.44 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 351 HIS 0.006 0.001 HIS D 191 PHE 0.019 0.001 PHE B 540 TYR 0.016 0.001 TYR C 471 ARG 0.003 0.000 ARG D 679 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 287 time to evaluate : 2.175 Fit side-chains REVERT: A 349 ASP cc_start: 0.7807 (t0) cc_final: 0.7561 (t0) REVERT: A 521 HIS cc_start: 0.7998 (m-70) cc_final: 0.7515 (p-80) REVERT: A 536 ASP cc_start: 0.8541 (t0) cc_final: 0.8326 (t0) REVERT: A 672 GLU cc_start: 0.8571 (tt0) cc_final: 0.8360 (tt0) REVERT: A 681 LYS cc_start: 0.8772 (tppt) cc_final: 0.8569 (tppt) REVERT: B 521 HIS cc_start: 0.7928 (m-70) cc_final: 0.7399 (p-80) REVERT: B 638 LEU cc_start: 0.8682 (mp) cc_final: 0.8401 (mp) REVERT: C 468 MET cc_start: 0.7354 (mtt) cc_final: 0.7138 (mtp) REVERT: C 525 TYR cc_start: 0.8435 (m-80) cc_final: 0.8108 (m-80) REVERT: D 525 TYR cc_start: 0.8420 (m-80) cc_final: 0.8081 (m-80) outliers start: 17 outliers final: 5 residues processed: 298 average time/residue: 0.2912 time to fit residues: 134.5366 Evaluate side-chains 266 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 261 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 153 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 10.0000 chunk 129 optimal weight: 0.0040 chunk 3 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS B 165 HIS C 165 HIS D 165 HIS D 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19760 Z= 0.162 Angle : 0.554 9.575 26804 Z= 0.270 Chirality : 0.036 0.152 3044 Planarity : 0.003 0.046 3292 Dihedral : 3.646 19.145 2588 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.92 % Favored : 91.57 % Rotamer: Outliers : 0.62 % Allowed : 14.33 % Favored : 85.05 % 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: 1.16 (0.19), residues: 2348 helix: 1.92 (0.14), residues: 1424 sheet: 1.69 (0.55), residues: 88 loop : -1.46 (0.24), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 386 HIS 0.005 0.001 HIS B 191 PHE 0.018 0.001 PHE B 540 TYR 0.017 0.001 TYR A 471 ARG 0.003 0.000 ARG C 679 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 271 time to evaluate : 2.117 Fit side-chains REVERT: A 165 HIS cc_start: 0.5667 (m170) cc_final: 0.5459 (m-70) REVERT: A 349 ASP cc_start: 0.7787 (t0) cc_final: 0.7543 (t0) REVERT: A 521 HIS cc_start: 0.8137 (m-70) cc_final: 0.7392 (p-80) REVERT: A 525 TYR cc_start: 0.8389 (m-80) cc_final: 0.8067 (m-80) REVERT: A 536 ASP cc_start: 0.8503 (t0) cc_final: 0.8218 (t0) REVERT: A 654 ASP cc_start: 0.7826 (m-30) cc_final: 0.7552 (p0) REVERT: A 672 GLU cc_start: 0.8574 (tt0) cc_final: 0.8217 (tt0) REVERT: B 335 TYR cc_start: 0.7831 (t80) cc_final: 0.7341 (t80) REVERT: B 521 HIS cc_start: 0.8021 (m-70) cc_final: 0.7170 (p-80) REVERT: B 525 TYR cc_start: 0.8420 (m-80) cc_final: 0.8065 (m-80) REVERT: B 654 ASP cc_start: 0.7829 (m-30) cc_final: 0.7558 (p0) REVERT: C 525 TYR cc_start: 0.8517 (m-80) cc_final: 0.8141 (m-80) REVERT: C 536 ASP cc_start: 0.8491 (t0) cc_final: 0.8105 (t0) REVERT: C 640 MET cc_start: 0.8692 (tmm) cc_final: 0.8210 (mmp) REVERT: D 525 TYR cc_start: 0.8498 (m-80) cc_final: 0.8136 (m-80) REVERT: D 654 ASP cc_start: 0.7818 (m-30) cc_final: 0.7542 (p0) outliers start: 13 outliers final: 9 residues processed: 275 average time/residue: 0.3015 time to fit residues: 127.5581 Evaluate side-chains 268 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 259 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS C 165 HIS D 165 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19760 Z= 0.259 Angle : 0.599 9.600 26804 Z= 0.296 Chirality : 0.038 0.155 3044 Planarity : 0.004 0.046 3292 Dihedral : 3.850 20.760 2588 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.65 % Favored : 90.67 % Rotamer: Outliers : 0.72 % Allowed : 15.87 % Favored : 83.41 % 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: 1.02 (0.19), residues: 2348 helix: 1.78 (0.14), residues: 1428 sheet: 2.37 (0.55), residues: 80 loop : -1.51 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 703 HIS 0.005 0.001 HIS C 251 PHE 0.020 0.002 PHE A 547 TYR 0.020 0.001 TYR A 471 ARG 0.005 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 266 time to evaluate : 2.349 Fit side-chains REVERT: A 521 HIS cc_start: 0.8108 (m-70) cc_final: 0.7335 (p-80) REVERT: A 525 TYR cc_start: 0.8472 (m-80) cc_final: 0.8138 (m-80) REVERT: A 672 GLU cc_start: 0.8567 (tt0) cc_final: 0.8335 (tt0) REVERT: B 525 TYR cc_start: 0.8548 (m-80) cc_final: 0.8152 (m-80) REVERT: B 645 MET cc_start: 0.8318 (mmm) cc_final: 0.7914 (mmm) REVERT: C 186 ASN cc_start: 0.8136 (m110) cc_final: 0.7936 (m110) REVERT: C 349 ASP cc_start: 0.8027 (t70) cc_final: 0.7496 (t70) REVERT: C 525 TYR cc_start: 0.8606 (m-80) cc_final: 0.8219 (m-80) REVERT: C 672 GLU cc_start: 0.8542 (tt0) cc_final: 0.8198 (tt0) REVERT: D 349 ASP cc_start: 0.7930 (t70) cc_final: 0.7691 (t70) REVERT: D 525 TYR cc_start: 0.8591 (m-80) cc_final: 0.8207 (m-80) outliers start: 15 outliers final: 12 residues processed: 270 average time/residue: 0.2987 time to fit residues: 123.9092 Evaluate side-chains 274 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 262 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 130 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 0.1980 chunk 192 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19760 Z= 0.138 Angle : 0.554 9.396 26804 Z= 0.270 Chirality : 0.036 0.160 3044 Planarity : 0.003 0.046 3292 Dihedral : 3.699 18.687 2588 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.54 % Favored : 91.95 % Rotamer: Outliers : 0.29 % Allowed : 17.07 % Favored : 82.64 % 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: 1.21 (0.19), residues: 2348 helix: 1.97 (0.14), residues: 1424 sheet: 1.70 (0.55), residues: 88 loop : -1.45 (0.24), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 657 HIS 0.003 0.001 HIS B 165 PHE 0.031 0.001 PHE D 540 TYR 0.015 0.001 TYR A 471 ARG 0.002 0.000 ARG A 679 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 273 time to evaluate : 2.295 Fit side-chains REVERT: A 286 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7417 (mm-40) REVERT: A 464 TRP cc_start: 0.7089 (m100) cc_final: 0.6834 (m100) REVERT: A 471 TYR cc_start: 0.7625 (p90) cc_final: 0.7403 (p90) REVERT: A 525 TYR cc_start: 0.8448 (m-80) cc_final: 0.8101 (m-80) REVERT: B 286 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7416 (mm-40) REVERT: B 471 TYR cc_start: 0.7500 (p90) cc_final: 0.7220 (p90) REVERT: B 525 TYR cc_start: 0.8508 (m-80) cc_final: 0.8164 (m-80) REVERT: B 645 MET cc_start: 0.8217 (mmm) cc_final: 0.7928 (mmm) REVERT: C 349 ASP cc_start: 0.7751 (t70) cc_final: 0.7467 (t70) REVERT: C 471 TYR cc_start: 0.7535 (p90) cc_final: 0.7238 (p90) REVERT: C 525 TYR cc_start: 0.8528 (m-80) cc_final: 0.8184 (m-80) REVERT: D 349 ASP cc_start: 0.7812 (t70) cc_final: 0.7476 (t70) REVERT: D 471 TYR cc_start: 0.7525 (p90) cc_final: 0.7226 (p90) REVERT: D 525 TYR cc_start: 0.8514 (m-80) cc_final: 0.8169 (m-80) outliers start: 6 outliers final: 5 residues processed: 274 average time/residue: 0.3076 time to fit residues: 127.9049 Evaluate side-chains 271 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 266 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 277 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 chunk 206 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS C 165 HIS D 165 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19760 Z= 0.159 Angle : 0.564 10.090 26804 Z= 0.272 Chirality : 0.036 0.161 3044 Planarity : 0.003 0.046 3292 Dihedral : 3.678 19.490 2588 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.35 % Favored : 91.14 % Rotamer: Outliers : 0.58 % Allowed : 17.50 % 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: 1.24 (0.19), residues: 2348 helix: 2.02 (0.14), residues: 1424 sheet: 1.62 (0.55), residues: 88 loop : -1.47 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 657 HIS 0.004 0.001 HIS D 191 PHE 0.028 0.001 PHE D 540 TYR 0.014 0.001 TYR A 471 ARG 0.003 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 268 time to evaluate : 2.123 Fit side-chains REVERT: A 174 LYS cc_start: 0.9169 (mmtt) cc_final: 0.8815 (mmmt) REVERT: A 464 TRP cc_start: 0.7131 (m100) cc_final: 0.6868 (m100) REVERT: A 471 TYR cc_start: 0.7637 (p90) cc_final: 0.7376 (p90) REVERT: A 525 TYR cc_start: 0.8469 (m-80) cc_final: 0.8120 (m-80) REVERT: B 174 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8811 (mmmt) REVERT: B 464 TRP cc_start: 0.7098 (m100) cc_final: 0.6839 (m100) REVERT: B 525 TYR cc_start: 0.8522 (m-80) cc_final: 0.8174 (m-80) REVERT: B 645 MET cc_start: 0.8175 (mmm) cc_final: 0.7937 (mmm) REVERT: C 525 TYR cc_start: 0.8549 (m-80) cc_final: 0.8197 (m-80) REVERT: D 174 LYS cc_start: 0.9146 (mmtt) cc_final: 0.8785 (mmmt) REVERT: D 525 TYR cc_start: 0.8543 (m-80) cc_final: 0.8175 (m-80) outliers start: 12 outliers final: 8 residues processed: 275 average time/residue: 0.2900 time to fit residues: 123.4110 Evaluate side-chains 265 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 257 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 153 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 191 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN D 165 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19760 Z= 0.185 Angle : 0.577 10.211 26804 Z= 0.280 Chirality : 0.037 0.164 3044 Planarity : 0.003 0.046 3292 Dihedral : 3.714 19.699 2588 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.35 % Favored : 91.14 % Rotamer: Outliers : 0.96 % Allowed : 17.31 % Favored : 81.73 % 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: 1.24 (0.19), residues: 2348 helix: 1.99 (0.14), residues: 1432 sheet: 1.87 (0.55), residues: 88 loop : -1.49 (0.24), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 657 HIS 0.004 0.001 HIS D 191 PHE 0.028 0.001 PHE A 540 TYR 0.016 0.001 TYR A 471 ARG 0.003 0.000 ARG C 679 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 258 time to evaluate : 2.232 Fit side-chains REVERT: A 174 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8805 (mmmt) REVERT: A 471 TYR cc_start: 0.7678 (p90) cc_final: 0.7409 (p90) REVERT: A 525 TYR cc_start: 0.8517 (m-80) cc_final: 0.8158 (m-80) REVERT: B 174 LYS cc_start: 0.9174 (mmtt) cc_final: 0.8816 (mmmt) REVERT: B 471 TYR cc_start: 0.7597 (p90) cc_final: 0.7354 (p90) REVERT: B 525 TYR cc_start: 0.8531 (m-80) cc_final: 0.8178 (m-80) REVERT: C 471 TYR cc_start: 0.7600 (p90) cc_final: 0.7354 (p90) REVERT: C 525 TYR cc_start: 0.8568 (m-80) cc_final: 0.8236 (m-80) REVERT: C 645 MET cc_start: 0.8087 (mmm) cc_final: 0.7747 (tpt) REVERT: D 174 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8806 (mmmt) REVERT: D 471 TYR cc_start: 0.7604 (p90) cc_final: 0.7347 (p90) REVERT: D 525 TYR cc_start: 0.8574 (m-80) cc_final: 0.8201 (m-80) outliers start: 20 outliers final: 14 residues processed: 264 average time/residue: 0.3043 time to fit residues: 123.0197 Evaluate side-chains 266 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 252 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 155 optimal weight: 0.0020 chunk 235 optimal weight: 0.6980 chunk 216 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN D 165 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19760 Z= 0.141 Angle : 0.567 10.102 26804 Z= 0.270 Chirality : 0.036 0.167 3044 Planarity : 0.003 0.046 3292 Dihedral : 3.629 18.807 2588 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.05 % Favored : 91.44 % Rotamer: Outliers : 0.67 % Allowed : 17.79 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 2348 helix: 2.10 (0.14), residues: 1424 sheet: 2.07 (0.55), residues: 88 loop : -1.42 (0.24), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 657 HIS 0.004 0.001 HIS C 191 PHE 0.028 0.001 PHE B 540 TYR 0.013 0.001 TYR A 471 ARG 0.004 0.000 ARG A 679 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 266 time to evaluate : 2.394 Fit side-chains REVERT: A 174 LYS cc_start: 0.9164 (mmtt) cc_final: 0.8802 (mmmt) REVERT: A 286 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7402 (mm-40) REVERT: A 525 TYR cc_start: 0.8497 (m-80) cc_final: 0.8158 (m-80) REVERT: B 174 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8800 (mmmt) REVERT: B 286 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7403 (mm-40) REVERT: B 464 TRP cc_start: 0.7068 (m100) cc_final: 0.6801 (m100) REVERT: B 525 TYR cc_start: 0.8528 (m-80) cc_final: 0.8251 (m-80) REVERT: C 286 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7408 (mm-40) REVERT: C 464 TRP cc_start: 0.7081 (m100) cc_final: 0.6816 (m100) REVERT: C 525 TYR cc_start: 0.8567 (m-80) cc_final: 0.8129 (m-80) REVERT: C 672 GLU cc_start: 0.8234 (tt0) cc_final: 0.7974 (tt0) REVERT: D 174 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8806 (mmmt) REVERT: D 286 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7407 (mm-40) REVERT: D 349 ASP cc_start: 0.7613 (t70) cc_final: 0.6993 (t0) REVERT: D 525 TYR cc_start: 0.8554 (m-80) cc_final: 0.8182 (m-80) REVERT: D 672 GLU cc_start: 0.8404 (tt0) cc_final: 0.7940 (tt0) outliers start: 14 outliers final: 10 residues processed: 274 average time/residue: 0.3035 time to fit residues: 128.9200 Evaluate side-chains 270 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 260 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 469 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 27 optimal weight: 0.0070 chunk 52 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 192 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.170748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114480 restraints weight = 29589.072| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.48 r_work: 0.3322 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19760 Z= 0.144 Angle : 0.564 10.438 26804 Z= 0.270 Chirality : 0.036 0.165 3044 Planarity : 0.003 0.046 3292 Dihedral : 3.593 18.682 2588 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.09 % Favored : 91.40 % Rotamer: Outliers : 0.58 % Allowed : 17.93 % Favored : 81.49 % 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: 1.40 (0.19), residues: 2348 helix: 2.12 (0.14), residues: 1424 sheet: 2.34 (0.56), residues: 88 loop : -1.43 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 657 HIS 0.004 0.001 HIS C 191 PHE 0.027 0.001 PHE C 540 TYR 0.014 0.001 TYR A 471 ARG 0.003 0.000 ARG B 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4127.22 seconds wall clock time: 75 minutes 16.61 seconds (4516.61 seconds total)