Starting phenix.real_space_refine on Mon Dec 11 21:39:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zje_14746/12_2023/7zje_14746.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zje_14746/12_2023/7zje_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_14746/12_2023/7zje_14746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zje_14746/12_2023/7zje_14746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zje_14746/12_2023/7zje_14746.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zje_14746/12_2023/7zje_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 9.47, per 1000 atoms: 0.49 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: 7.41 Conformation dependent library (CDL) restraints added in 3.7 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: 1.82 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: 5.29 Time building geometry restraints manager: 7.95 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: 2.470 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: 10.530 Check model and map are aligned: 0.270 Set scattering table: 0.190 Process input model: 47.490 Find NCS groups from input model: 1.140 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.030 ------------------------------------------------------------------------------- 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 : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 308 average time/residue: 0.2746 time to fit residues: 135.6919 Evaluate side-chains 258 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 2.004 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8447 ------------------------------------------------------------------------------- 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: 0.7705 moved from start: 0.0937 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 : 0.542 9.255 26804 Z= 0.264 Chirality : 0.036 0.130 3044 Planarity : 0.004 0.044 3292 Dihedral : 3.584 17.293 2588 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.53 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: 1.11 (0.19), residues: 2348 helix: 1.83 (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 C 386 HIS 0.003 0.001 HIS C 165 PHE 0.012 0.001 PHE B 547 TYR 0.021 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 293 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 280 time to evaluate : 2.212 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 285 average time/residue: 0.2872 time to fit residues: 130.4563 Evaluate side-chains 275 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 270 time to evaluate : 2.042 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1651 time to fit residues: 4.4420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 178 optimal weight: 0.0010 chunk 145 optimal weight: 0.6980 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 0.2980 chunk 231 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 521 HIS ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 HIS C 165 HIS ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19760 Z= 0.134 Angle : 0.531 8.567 26804 Z= 0.257 Chirality : 0.036 0.134 3044 Planarity : 0.003 0.044 3292 Dihedral : 3.553 17.500 2588 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.18 % Favored : 91.31 % Rotamer: Outliers : 0.38 % Allowed : 10.91 % Favored : 88.70 % 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: 1.18 (0.19), residues: 2348 helix: 1.93 (0.14), residues: 1420 sheet: 1.75 (0.56), residues: 88 loop : -1.41 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 386 HIS 0.003 0.001 HIS C 165 PHE 0.012 0.001 PHE D 547 TYR 0.018 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 308 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 300 time to evaluate : 2.091 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 307 average time/residue: 0.2972 time to fit residues: 142.4856 Evaluate side-chains 268 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 2.193 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1703 time to fit residues: 3.3163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 144 optimal weight: 0.0770 chunk 215 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 204 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.7342 ------------------------------------------------------------------------------- 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 C 521 HIS D 165 HIS D 521 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1378 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= 0.151 Angle : 0.539 8.822 26804 Z= 0.263 Chirality : 0.037 0.143 3044 Planarity : 0.003 0.045 3292 Dihedral : 3.591 18.129 2588 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.45 % Favored : 92.04 % Rotamer: Outliers : 0.72 % Allowed : 11.63 % Favored : 87.64 % 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: 1.96 (0.14), residues: 1420 sheet: 1.74 (0.56), residues: 88 loop : -1.42 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 386 HIS 0.005 0.001 HIS D 191 PHE 0.019 0.001 PHE C 540 TYR 0.016 0.001 TYR C 471 ARG 0.003 0.000 ARG B 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 293 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 278 time to evaluate : 2.138 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 285 average time/residue: 0.2941 time to fit residues: 131.9691 Evaluate side-chains 270 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 263 time to evaluate : 2.205 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1780 time to fit residues: 5.8022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 3 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 194 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 C 186 ASN C 438 HIS D 165 HIS D 186 ASN D 438 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19760 Z= 0.257 Angle : 0.598 9.202 26804 Z= 0.297 Chirality : 0.039 0.158 3044 Planarity : 0.004 0.046 3292 Dihedral : 3.856 21.414 2588 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.52 % Favored : 90.80 % Rotamer: Outliers : 0.77 % Allowed : 14.23 % Favored : 85.00 % 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: 0.95 (0.19), residues: 2348 helix: 1.73 (0.14), residues: 1424 sheet: 1.45 (0.56), residues: 88 loop : -1.46 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 703 HIS 0.005 0.001 HIS B 251 PHE 0.019 0.002 PHE B 540 TYR 0.020 0.001 TYR B 471 ARG 0.002 0.000 ARG D 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 291 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 275 time to evaluate : 2.252 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 284 average time/residue: 0.3046 time to fit residues: 134.1660 Evaluate side-chains 275 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 270 time to evaluate : 2.252 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1835 time to fit residues: 4.8646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 119 optimal weight: 30.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS C 521 HIS D 521 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19760 Z= 0.235 Angle : 0.593 9.940 26804 Z= 0.291 Chirality : 0.038 0.149 3044 Planarity : 0.003 0.046 3292 Dihedral : 3.870 20.659 2588 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.48 % Favored : 90.84 % Rotamer: Outliers : 0.48 % Allowed : 15.62 % Favored : 83.89 % 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: 0.89 (0.19), residues: 2348 helix: 1.70 (0.14), residues: 1420 sheet: 1.56 (0.55), residues: 88 loop : -1.53 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 386 HIS 0.004 0.001 HIS C 251 PHE 0.021 0.001 PHE A 540 TYR 0.018 0.001 TYR B 471 ARG 0.002 0.000 ARG D 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 287 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 277 time to evaluate : 2.212 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 277 average time/residue: 0.3158 time to fit residues: 134.3048 Evaluate side-chains 278 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 270 time to evaluate : 2.166 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1737 time to fit residues: 5.7278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 130 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 127 optimal weight: 0.1980 chunk 227 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 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 165 HIS A 521 HIS B 165 HIS C 165 HIS C 186 ASN C 521 HIS D 165 HIS D 186 ASN D 521 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2000 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= 0.164 Angle : 0.575 9.344 26804 Z= 0.279 Chirality : 0.037 0.152 3044 Planarity : 0.003 0.046 3292 Dihedral : 3.786 19.851 2588 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.18 % Favored : 91.31 % Rotamer: Outliers : 0.19 % Allowed : 16.97 % Favored : 82.84 % 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: 1.82 (0.14), residues: 1424 sheet: 1.57 (0.55), residues: 88 loop : -1.55 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 657 HIS 0.004 0.001 HIS A 165 PHE 0.030 0.001 PHE C 540 TYR 0.020 0.001 TYR D 471 ARG 0.003 0.000 ARG B 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 272 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 268 time to evaluate : 2.180 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 270 average time/residue: 0.3184 time to fit residues: 130.4066 Evaluate side-chains 261 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.117 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.001 > 50: distance: 48 - 52: 3.698 distance: 52 - 53: 7.418 distance: 53 - 54: 7.553 distance: 54 - 55: 25.036 distance: 54 - 60: 27.556 distance: 56 - 57: 4.280 distance: 57 - 58: 8.602 distance: 57 - 59: 5.510 distance: 60 - 61: 6.897 distance: 61 - 62: 18.747 distance: 62 - 63: 17.383 distance: 62 - 64: 13.186 distance: 64 - 65: 3.577 distance: 65 - 66: 3.947 distance: 65 - 68: 5.145 distance: 66 - 72: 6.237 distance: 68 - 69: 4.766 distance: 69 - 70: 3.308 distance: 69 - 71: 3.266 distance: 73 - 74: 3.331 distance: 73 - 76: 4.209 distance: 74 - 75: 3.516 distance: 74 - 79: 3.002 distance: 75 - 104: 5.563 distance: 76 - 78: 6.441 distance: 80 - 81: 4.528 distance: 80 - 83: 3.814 distance: 81 - 82: 3.965 distance: 82 - 109: 6.384 distance: 83 - 84: 5.379 distance: 83 - 85: 3.965 distance: 90 - 91: 4.861 distance: 91 - 92: 3.315 distance: 91 - 93: 3.359 distance: 95 - 96: 3.639 distance: 95 - 98: 4.846 distance: 96 - 97: 3.234 distance: 96 - 104: 3.891 distance: 97 - 124: 4.128 distance: 99 - 100: 5.389 distance: 99 - 101: 3.067 distance: 100 - 102: 4.021 distance: 101 - 103: 3.813 distance: 102 - 103: 3.053 distance: 105 - 106: 3.615 distance: 105 - 108: 4.117 distance: 106 - 107: 5.274 distance: 106 - 109: 5.809 distance: 107 - 131: 4.190 distance: 110 - 111: 3.810 distance: 110 - 113: 3.254 distance: 111 - 112: 5.353 distance: 111 - 117: 5.553 distance: 113 - 114: 4.756 distance: 114 - 115: 9.938 distance: 114 - 116: 8.461 distance: 118 - 121: 3.084 distance: 121 - 122: 3.910 distance: 121 - 123: 4.026 distance: 205 - 215: 3.337