Starting phenix.real_space_refine on Wed Mar 20 21:05:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3v_32994/03_2024/7x3v_32994.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3v_32994/03_2024/7x3v_32994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3v_32994/03_2024/7x3v_32994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3v_32994/03_2024/7x3v_32994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3v_32994/03_2024/7x3v_32994.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3v_32994/03_2024/7x3v_32994.pdb" } resolution = 3.09 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11879 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 27 5.16 5 C 9716 2.51 5 N 3053 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 48": "OD1" <-> "OD2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "U TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 246": "OD1" <-> "OD2" Residue "U TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 456": "OE1" <-> "OE2" Residue "U PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 481": "OE1" <-> "OE2" Residue "U PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 742": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16799 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2978 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3008 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "U" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4840 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 38, 'TRANS': 551} Chain breaks: 1 Time building chain proxies: 9.93, per 1000 atoms: 0.59 Number of scatterers: 16799 At special positions: 0 Unit cell: (139.642, 124.487, 146.137, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 292 15.00 O 3711 8.00 N 3053 7.00 C 9716 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: 7.90 Conformation dependent library (CDL) restraints added in 1.8 seconds 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2564 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 11 sheets defined 64.6% alpha, 2.7% beta 144 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 6.99 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.511A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.636A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.535A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.541A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.546A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.526A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.548A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.757A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.540A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.515A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.521A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 178 through 192 Processing helix chain 'U' and resid 193 through 196 Processing helix chain 'U' and resid 197 through 202 removed outlier: 3.566A pdb=" N GLN U 201 " --> pdb=" O HIS U 197 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN U 202 " --> pdb=" O SER U 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 197 through 202' Processing helix chain 'U' and resid 204 through 213 Processing helix chain 'U' and resid 237 through 241 Processing helix chain 'U' and resid 243 through 267 removed outlier: 3.588A pdb=" N ILE U 247 " --> pdb=" O ALA U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 283 through 288 Processing helix chain 'U' and resid 295 through 310 removed outlier: 4.472A pdb=" N ARG U 307 " --> pdb=" O ARG U 303 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU U 308 " --> pdb=" O LEU U 304 " (cutoff:3.500A) Processing helix chain 'U' and resid 312 through 316 removed outlier: 3.564A pdb=" N ARG U 316 " --> pdb=" O ARG U 313 " (cutoff:3.500A) Processing helix chain 'U' and resid 368 through 376 removed outlier: 6.065A pdb=" N ARG U 373 " --> pdb=" O LEU U 370 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU U 374 " --> pdb=" O TYR U 371 " (cutoff:3.500A) Processing helix chain 'U' and resid 384 through 403 Processing helix chain 'U' and resid 403 through 415 removed outlier: 3.697A pdb=" N TYR U 411 " --> pdb=" O HIS U 407 " (cutoff:3.500A) Processing helix chain 'U' and resid 430 through 435 Processing helix chain 'U' and resid 436 through 460 Processing helix chain 'U' and resid 461 through 469 removed outlier: 3.598A pdb=" N LYS U 469 " --> pdb=" O VAL U 465 " (cutoff:3.500A) Processing helix chain 'U' and resid 474 through 492 removed outlier: 4.598A pdb=" N LEU U 480 " --> pdb=" O LEU U 476 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 510 removed outlier: 4.341A pdb=" N ASP U 499 " --> pdb=" O LYS U 495 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU U 500 " --> pdb=" O SER U 496 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU U 502 " --> pdb=" O LYS U 498 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE U 503 " --> pdb=" O ASP U 499 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASP U 507 " --> pdb=" O PHE U 503 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS U 508 " --> pdb=" O SER U 504 " (cutoff:3.500A) Processing helix chain 'U' and resid 524 through 528 removed outlier: 3.679A pdb=" N SER U 527 " --> pdb=" O ASN U 524 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU U 528 " --> pdb=" O PRO U 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 524 through 528' Processing helix chain 'U' and resid 568 through 581 Processing helix chain 'U' and resid 585 through 592 Processing helix chain 'U' and resid 607 through 618 Processing helix chain 'U' and resid 633 through 649 removed outlier: 3.823A pdb=" N TYR U 646 " --> pdb=" O GLU U 642 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS U 647 " --> pdb=" O PHE U 643 " (cutoff:3.500A) Processing helix chain 'U' and resid 651 through 656 Processing helix chain 'U' and resid 681 through 686 removed outlier: 3.616A pdb=" N ILE U 685 " --> pdb=" O ASN U 681 " (cutoff:3.500A) Processing helix chain 'U' and resid 695 through 727 removed outlier: 4.548A pdb=" N ALA U 699 " --> pdb=" O LYS U 695 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE U 715 " --> pdb=" O SER U 711 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE U 716 " --> pdb=" O ASP U 712 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL U 725 " --> pdb=" O GLU U 721 " (cutoff:3.500A) Processing helix chain 'U' and resid 732 through 743 removed outlier: 3.896A pdb=" N GLN U 736 " --> pdb=" O PRO U 732 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE U 740 " --> pdb=" O GLN U 736 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.076A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.302A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.745A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.016A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.142A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'U' and resid 174 through 175 removed outlier: 6.824A pdb=" N LEU U 603 " --> pdb=" O LEU U 630 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY U 547 " --> pdb=" O ARG U 542 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ARG U 542 " --> pdb=" O GLY U 547 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE U 549 " --> pdb=" O LEU U 540 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 8.59 Time building geometry restraints manager: 8.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2752 1.32 - 1.44: 5689 1.44 - 1.56: 8657 1.56 - 1.68: 582 1.68 - 1.80: 48 Bond restraints: 17728 Sorted by residual: bond pdb=" N ARG H 30 " pdb=" CA ARG H 30 " ideal model delta sigma weight residual 1.454 1.484 -0.029 1.17e-02 7.31e+03 6.35e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.52e+00 bond pdb=" CG1 ILE H 58 " pdb=" CD1 ILE H 58 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.22e+00 bond pdb=" CB GLN A 76 " pdb=" CG GLN A 76 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.93e+00 bond pdb=" CB ARG B 35 " pdb=" CG ARG B 35 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.61e+00 ... (remaining 17723 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.33: 1470 105.33 - 112.51: 9723 112.51 - 119.70: 5901 119.70 - 126.88: 7299 126.88 - 134.06: 827 Bond angle restraints: 25220 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.71 109.00 4.71 9.50e-01 1.11e+00 2.46e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 124.55 -4.35 1.50e+00 4.44e-01 8.39e+00 angle pdb=" N THR U 155 " pdb=" CA THR U 155 " pdb=" CB THR U 155 " ideal model delta sigma weight residual 113.65 109.54 4.11 1.47e+00 4.63e-01 7.83e+00 angle pdb=" N THR U 155 " pdb=" CA THR U 155 " pdb=" C THR U 155 " ideal model delta sigma weight residual 113.72 109.53 4.19 1.52e+00 4.33e-01 7.59e+00 angle pdb=" NE ARG D 76 " pdb=" CZ ARG D 76 " pdb=" NH1 ARG D 76 " ideal model delta sigma weight residual 121.50 118.84 2.66 1.00e+00 1.00e+00 7.09e+00 ... (remaining 25215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 8412 34.99 - 69.99: 1507 69.99 - 104.98: 26 104.98 - 139.98: 1 139.98 - 174.97: 3 Dihedral angle restraints: 9949 sinusoidal: 5990 harmonic: 3959 Sorted by residual: dihedral pdb=" CA ASN U 269 " pdb=" C ASN U 269 " pdb=" N PHE U 270 " pdb=" CA PHE U 270 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLU U 268 " pdb=" C GLU U 268 " pdb=" N ASN U 269 " pdb=" CA ASN U 269 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TYR U 355 " pdb=" C TYR U 355 " pdb=" N THR U 356 " pdb=" CA THR U 356 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 9946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1421 0.033 - 0.067: 937 0.067 - 0.100: 381 0.100 - 0.133: 82 0.133 - 0.166: 15 Chirality restraints: 2836 Sorted by residual: chirality pdb=" CA PRO B 32 " pdb=" N PRO B 32 " pdb=" C PRO B 32 " pdb=" CB PRO B 32 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CG LEU U 235 " pdb=" CB LEU U 235 " pdb=" CD1 LEU U 235 " pdb=" CD2 LEU U 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" C4' DG J 68 " pdb=" C5' DG J 68 " pdb=" O4' DG J 68 " pdb=" C3' DG J 68 " both_signs ideal model delta sigma weight residual False -2.53 -2.37 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 2833 not shown) Planarity restraints: 2201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE U 151 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO U 152 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO U 152 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO U 152 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO H 100 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO D 100 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " 0.035 5.00e-02 4.00e+02 ... (remaining 2198 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 671 2.69 - 3.24: 15572 3.24 - 3.79: 29866 3.79 - 4.35: 39670 4.35 - 4.90: 57576 Nonbonded interactions: 143355 Sorted by model distance: nonbonded pdb=" OG1 THR U 426 " pdb=" OE1 GLN U 427 " model vdw 2.135 2.440 nonbonded pdb=" NZ LYS U 418 " pdb=" O ASP U 419 " model vdw 2.140 2.520 nonbonded pdb=" NZ LYS U 445 " pdb=" O LYS U 498 " model vdw 2.209 2.520 nonbonded pdb=" O SER U 401 " pdb=" ND1 HIS U 407 " model vdw 2.243 2.520 nonbonded pdb=" O PRO U 430 " pdb=" OG1 THR U 433 " model vdw 2.246 2.440 ... (remaining 143350 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 14.120 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 51.640 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.011 0.081 17728 Z= 0.631 Angle : 0.771 8.293 25220 Z= 0.448 Chirality : 0.048 0.166 2836 Planarity : 0.006 0.072 2201 Dihedral : 25.591 174.973 7385 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1331 helix: 0.49 (0.18), residues: 808 sheet: -0.60 (1.25), residues: 10 loop : -2.21 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 509 HIS 0.008 0.002 HIS U 555 PHE 0.033 0.003 PHE U 208 TYR 0.038 0.003 TYR G 50 ARG 0.014 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.527 Fit side-chains REVERT: G 64 GLU cc_start: 0.8599 (tt0) cc_final: 0.8370 (tt0) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3175 time to fit residues: 51.7205 Evaluate side-chains 109 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9990 chunk 120 optimal weight: 0.0670 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 592 ASN ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17728 Z= 0.182 Angle : 0.577 7.219 25220 Z= 0.334 Chirality : 0.036 0.131 2836 Planarity : 0.005 0.062 2201 Dihedral : 28.788 172.559 4673 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.17 % Allowed : 3.45 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.23), residues: 1331 helix: 1.59 (0.19), residues: 809 sheet: None (None), residues: 0 loop : -1.87 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U 509 HIS 0.003 0.001 HIS E 113 PHE 0.016 0.001 PHE U 539 TYR 0.018 0.001 TYR H 37 ARG 0.006 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.427 Fit side-chains REVERT: D 44 GLN cc_start: 0.8146 (mt0) cc_final: 0.7903 (mt0) REVERT: G 64 GLU cc_start: 0.8554 (tt0) cc_final: 0.8260 (tt0) outliers start: 2 outliers final: 2 residues processed: 117 average time/residue: 0.3006 time to fit residues: 52.9886 Evaluate side-chains 114 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 113 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 44 GLN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17728 Z= 0.253 Angle : 0.572 7.203 25220 Z= 0.332 Chirality : 0.036 0.131 2836 Planarity : 0.005 0.055 2201 Dihedral : 28.743 172.710 4673 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.34 % Allowed : 5.78 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1331 helix: 1.80 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.74 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 627 HIS 0.004 0.001 HIS E 113 PHE 0.014 0.001 PHE U 539 TYR 0.015 0.001 TYR H 37 ARG 0.003 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 1.622 Fit side-chains REVERT: C 73 ASN cc_start: 0.8571 (t0) cc_final: 0.8294 (t0) REVERT: G 64 GLU cc_start: 0.8583 (tt0) cc_final: 0.8311 (tt0) outliers start: 4 outliers final: 3 residues processed: 117 average time/residue: 0.3081 time to fit residues: 53.9821 Evaluate side-chains 116 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17728 Z= 0.207 Angle : 0.552 7.093 25220 Z= 0.320 Chirality : 0.035 0.129 2836 Planarity : 0.004 0.055 2201 Dihedral : 28.620 173.246 4673 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.60 % Allowed : 6.47 % Favored : 92.93 % 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: 0.96 (0.24), residues: 1331 helix: 1.97 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.60 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 627 HIS 0.003 0.001 HIS E 113 PHE 0.013 0.001 PHE U 539 TYR 0.014 0.001 TYR U 238 ARG 0.003 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 1.425 Fit side-chains REVERT: C 73 ASN cc_start: 0.8627 (t0) cc_final: 0.8355 (t0) REVERT: G 64 GLU cc_start: 0.8581 (tt0) cc_final: 0.8323 (tt0) outliers start: 7 outliers final: 5 residues processed: 116 average time/residue: 0.3039 time to fit residues: 53.9174 Evaluate side-chains 118 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain U residue 571 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 114 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 0.0070 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 592 ASN ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17728 Z= 0.193 Angle : 0.540 7.097 25220 Z= 0.313 Chirality : 0.035 0.130 2836 Planarity : 0.004 0.052 2201 Dihedral : 28.424 175.615 4673 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.69 % Allowed : 7.50 % Favored : 91.81 % 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 (0.24), residues: 1331 helix: 2.15 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.45 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U 627 HIS 0.003 0.001 HIS U 407 PHE 0.013 0.001 PHE U 590 TYR 0.014 0.001 TYR U 238 ARG 0.003 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.404 Fit side-chains REVERT: C 73 ASN cc_start: 0.8592 (t0) cc_final: 0.8362 (t0) REVERT: D 37 TYR cc_start: 0.9379 (m-80) cc_final: 0.9029 (m-80) REVERT: G 64 GLU cc_start: 0.8567 (tt0) cc_final: 0.8314 (tt0) outliers start: 8 outliers final: 7 residues processed: 120 average time/residue: 0.2934 time to fit residues: 53.4707 Evaluate side-chains 122 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 590 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17728 Z= 0.254 Angle : 0.554 7.041 25220 Z= 0.320 Chirality : 0.036 0.140 2836 Planarity : 0.004 0.052 2201 Dihedral : 28.554 178.542 4673 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.03 % Allowed : 8.10 % Favored : 90.86 % 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 (0.24), residues: 1331 helix: 2.08 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 627 HIS 0.003 0.001 HIS E 113 PHE 0.011 0.001 PHE U 590 TYR 0.023 0.001 TYR U 300 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.504 Fit side-chains REVERT: C 73 ASN cc_start: 0.8683 (t0) cc_final: 0.8466 (t0) REVERT: G 64 GLU cc_start: 0.8598 (tt0) cc_final: 0.8339 (tt0) outliers start: 12 outliers final: 9 residues processed: 121 average time/residue: 0.2981 time to fit residues: 54.5162 Evaluate side-chains 124 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain U residue 240 ASP Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 590 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 153 optimal weight: 0.0670 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.004 0.053 17728 Z= 0.218 Angle : 0.546 6.964 25220 Z= 0.317 Chirality : 0.035 0.133 2836 Planarity : 0.004 0.053 2201 Dihedral : 28.543 178.661 4673 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.03 % Allowed : 8.45 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.24), residues: 1331 helix: 2.11 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.41 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 627 HIS 0.003 0.001 HIS E 113 PHE 0.012 0.001 PHE U 590 TYR 0.012 0.001 TYR U 238 ARG 0.003 0.000 ARG U 553 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.794 Fit side-chains REVERT: C 73 ASN cc_start: 0.8685 (t0) cc_final: 0.8469 (t0) REVERT: G 64 GLU cc_start: 0.8596 (tt0) cc_final: 0.8341 (tt0) outliers start: 12 outliers final: 10 residues processed: 121 average time/residue: 0.3027 time to fit residues: 54.7819 Evaluate side-chains 124 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain U residue 240 ASP Chi-restraints excluded: chain U residue 543 VAL Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 590 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17728 Z= 0.212 Angle : 0.545 6.963 25220 Z= 0.316 Chirality : 0.035 0.131 2836 Planarity : 0.004 0.053 2201 Dihedral : 28.531 178.753 4673 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.03 % Allowed : 8.88 % Favored : 90.09 % 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: 1.23 (0.24), residues: 1331 helix: 2.13 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.39 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 627 HIS 0.003 0.001 HIS E 113 PHE 0.012 0.001 PHE U 590 TYR 0.012 0.001 TYR U 238 ARG 0.003 0.000 ARG U 739 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.173 Fit side-chains REVERT: C 73 ASN cc_start: 0.8683 (t0) cc_final: 0.8465 (t0) REVERT: G 64 GLU cc_start: 0.8597 (tt0) cc_final: 0.8341 (tt0) outliers start: 12 outliers final: 10 residues processed: 121 average time/residue: 0.2840 time to fit residues: 51.6818 Evaluate side-chains 124 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain U residue 240 ASP Chi-restraints excluded: chain U residue 543 VAL Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 590 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 151 optimal weight: 0.0370 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 606 HIS ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17728 Z= 0.334 Angle : 0.583 7.011 25220 Z= 0.336 Chirality : 0.038 0.130 2836 Planarity : 0.005 0.052 2201 Dihedral : 28.723 179.348 4673 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.21 % Allowed : 8.79 % Favored : 90.00 % 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: 1.04 (0.24), residues: 1331 helix: 1.97 (0.19), residues: 809 sheet: None (None), residues: 0 loop : -1.46 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 509 HIS 0.004 0.001 HIS E 113 PHE 0.013 0.002 PHE U 590 TYR 0.023 0.001 TYR U 300 ARG 0.006 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.268 Fit side-chains REVERT: G 64 GLU cc_start: 0.8613 (tt0) cc_final: 0.8342 (tt0) REVERT: U 606 HIS cc_start: 0.6428 (OUTLIER) cc_final: 0.6093 (t70) outliers start: 14 outliers final: 11 residues processed: 124 average time/residue: 0.3127 time to fit residues: 58.2471 Evaluate side-chains 128 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain U residue 240 ASP Chi-restraints excluded: chain U residue 543 VAL Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 590 PHE Chi-restraints excluded: chain U residue 606 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 606 HIS ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17728 Z= 0.302 Angle : 0.573 7.043 25220 Z= 0.331 Chirality : 0.037 0.131 2836 Planarity : 0.005 0.053 2201 Dihedral : 28.683 178.968 4673 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.12 % Allowed : 8.79 % Favored : 90.09 % 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: 1.04 (0.24), residues: 1331 helix: 1.96 (0.19), residues: 809 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 627 HIS 0.004 0.001 HIS U 606 PHE 0.012 0.001 PHE U 590 TYR 0.010 0.001 TYR U 238 ARG 0.005 0.000 ARG C 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.452 Fit side-chains REVERT: G 64 GLU cc_start: 0.8616 (tt0) cc_final: 0.8353 (tt0) REVERT: U 606 HIS cc_start: 0.6511 (OUTLIER) cc_final: 0.6129 (t70) outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 0.3191 time to fit residues: 59.2159 Evaluate side-chains 127 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain U residue 240 ASP Chi-restraints excluded: chain U residue 440 THR Chi-restraints excluded: chain U residue 543 VAL Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 590 PHE Chi-restraints excluded: chain U residue 606 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 606 HIS ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.110605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.070249 restraints weight = 40959.138| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.03 r_work: 0.2828 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17728 Z= 0.187 Angle : 0.548 7.011 25220 Z= 0.318 Chirality : 0.035 0.137 2836 Planarity : 0.004 0.053 2201 Dihedral : 28.606 178.973 4673 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.03 % Allowed : 8.79 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.24), residues: 1331 helix: 2.08 (0.19), residues: 809 sheet: None (None), residues: 0 loop : -1.36 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP U 627 HIS 0.012 0.001 HIS U 606 PHE 0.012 0.001 PHE U 590 TYR 0.025 0.001 TYR U 300 ARG 0.003 0.000 ARG C 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2835.52 seconds wall clock time: 52 minutes 27.76 seconds (3147.76 seconds total)