Starting phenix.real_space_refine on Sat Dec 9 09:46:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/12_2023/6c5v_7344_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/12_2023/6c5v_7344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/12_2023/6c5v_7344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/12_2023/6c5v_7344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/12_2023/6c5v_7344_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/12_2023/6c5v_7344_updated.pdb" } resolution = 4.8 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= 0.007 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 58 5.16 5 C 6787 2.51 5 N 1749 2.21 5 O 2055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10649 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5101 Classifications: {'peptide': 655} Link IDs: {'PTRANS': 26, 'TRANS': 628} Chain: "B" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 2 Chain: "C" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1435 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "H" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1615 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1598 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 194} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.94, per 1000 atoms: 0.65 Number of scatterers: 10649 At special positions: 0 Unit cell: (137.36, 116.96, 127.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2055 8.00 N 1749 7.00 C 6787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 335 " distance=2.04 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 615 " distance=2.04 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 56 " distance=2.05 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 138 " distance=2.02 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 115 " distance=2.08 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 216 " distance=2.01 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 208 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.11 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 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A 707 " - " ASN A 435 " " NAG A 708 " - " ASN A 549 " " NAG A 709 " - " ASN A 664 " " NAG B 201 " - " ASN B 44 " " NAG B 202 " - " ASN B 53 " " NAG C 301 " - " ASN C 64 " " NAG C 302 " - " ASN C 98 " " NAG C 303 " - " ASN C 173 " " NAG D 1 " - " ASN A 60 " Time building additional restraints: 4.24 Conformation dependent library (CDL) restraints added in 2.0 seconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 17 sheets defined 26.7% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 41 through 44 No H-bonds generated for 'chain 'A' and resid 41 through 44' Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.922A pdb=" N ASN A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 258 through 274 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 285 through 306 Processing helix chain 'A' and resid 315 through 335 removed outlier: 3.717A pdb=" N ILE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 removed outlier: 3.522A pdb=" N THR A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 4.748A pdb=" N GLY A 365 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 390 through 404 Processing helix chain 'A' and resid 415 through 433 removed outlier: 3.700A pdb=" N HIS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 471 through 474 No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 477 through 480 Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 503 through 516 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 583 through 585 No H-bonds generated for 'chain 'A' and resid 583 through 585' Processing helix chain 'A' and resid 637 through 645 Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 82 through 95 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'C' and resid 67 through 70 No H-bonds generated for 'chain 'C' and resid 67 through 70' Processing helix chain 'C' and resid 125 through 133 removed outlier: 4.241A pdb=" N PHE C 129 " --> pdb=" O TRP C 125 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 133 " --> pdb=" O PHE C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 155 removed outlier: 3.838A pdb=" N ASN C 155 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 192 through 196 Processing helix chain 'H' and resid 207 through 209 No H-bonds generated for 'chain 'H' and resid 207 through 209' Processing helix chain 'L' and resid 27 through 29 No H-bonds generated for 'chain 'L' and resid 27 through 29' Processing helix chain 'L' and resid 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 93 through 95 No H-bonds generated for 'chain 'L' and resid 93 through 95' Processing helix chain 'L' and resid 126 through 130 Processing helix chain 'L' and resid 186 through 191 Processing sheet with id= A, first strand: chain 'A' and resid 23 through 29 Processing sheet with id= B, first strand: chain 'A' and resid 100 through 102 Processing sheet with id= C, first strand: chain 'A' and resid 339 through 341 removed outlier: 3.608A pdb=" N ALA A 172 " --> pdb=" O MET A 179 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 228 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A 217 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 578 through 583 Processing sheet with id= E, first strand: chain 'A' and resid 667 through 669 removed outlier: 5.649A pdb=" N ASP A 623 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU A 628 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.749A pdb=" N LEU A 151 " --> pdb=" O MET A 137 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 50 Processing sheet with id= H, first strand: chain 'C' and resid 109 through 111 removed outlier: 3.589A pdb=" N CYS C 214 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.643A pdb=" N ASP H 10 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.862A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER H 185 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 157 through 160 Processing sheet with id= M, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.127A pdb=" N LYS L 106 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL L 12 " --> pdb=" O LYS L 106 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR L 108 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 18 through 23 Processing sheet with id= O, first strand: chain 'L' and resid 88 through 91 Processing sheet with id= P, first strand: chain 'L' and resid 118 through 122 Processing sheet with id= Q, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.365A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1035 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: 3.12 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2582 1.33 - 1.46: 3189 1.46 - 1.59: 5054 1.59 - 1.72: 2 1.72 - 1.85: 82 Bond restraints: 10909 Sorted by residual: bond pdb=" CB LEU A 20 " pdb=" CG LEU A 20 " ideal model delta sigma weight residual 1.530 1.605 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C6 MAN D 6 " pdb=" O6 MAN D 6 " ideal model delta sigma weight residual 1.407 1.479 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " ideal model delta sigma weight residual 1.526 1.455 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C6 BMA D 3 " pdb=" O6 BMA D 3 " ideal model delta sigma weight residual 1.411 1.482 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C3 BMA D 3 " pdb=" O3 BMA D 3 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 10904 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.35: 388 106.35 - 113.26: 5959 113.26 - 120.16: 3689 120.16 - 127.07: 4722 127.07 - 133.98: 98 Bond angle restraints: 14856 Sorted by residual: angle pdb=" CD1 LEU B 74 " pdb=" CG LEU B 74 " pdb=" CD2 LEU B 74 " ideal model delta sigma weight residual 110.80 133.38 -22.58 2.20e+00 2.07e-01 1.05e+02 angle pdb=" C ASP C 56 " pdb=" N PRO C 57 " pdb=" CA PRO C 57 " ideal model delta sigma weight residual 119.66 126.38 -6.72 7.30e-01 1.88e+00 8.49e+01 angle pdb=" CD1 LEU A 20 " pdb=" CG LEU A 20 " pdb=" CD2 LEU A 20 " ideal model delta sigma weight residual 110.80 130.49 -19.69 2.20e+00 2.07e-01 8.01e+01 angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 126.01 -6.35 7.20e-01 1.93e+00 7.78e+01 angle pdb=" C PRO C 57 " pdb=" N PRO C 58 " pdb=" CA PRO C 58 " ideal model delta sigma weight residual 119.66 125.85 -6.19 7.30e-01 1.88e+00 7.20e+01 ... (remaining 14851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 6294 15.63 - 31.26: 191 31.26 - 46.89: 62 46.89 - 62.51: 38 62.51 - 78.14: 9 Dihedral angle restraints: 6594 sinusoidal: 2675 harmonic: 3919 Sorted by residual: dihedral pdb=" CB CYS A 278 " pdb=" SG CYS A 278 " pdb=" SG CYS A 335 " pdb=" CB CYS A 335 " ideal model delta sinusoidal sigma weight residual -86.00 -130.64 44.64 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CA CYS A 534 " pdb=" CB CYS A 534 " pdb=" SG CYS A 534 " pdb=" SG CYS A 587 " ideal model delta sinusoidal sigma weight residual -73.00 -2.44 -70.56 1 2.00e+01 2.50e-03 1.60e+01 dihedral pdb=" CA VAL C 201 " pdb=" C VAL C 201 " pdb=" N PRO C 202 " pdb=" CA PRO C 202 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 6591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1541 0.116 - 0.232: 180 0.232 - 0.349: 11 0.349 - 0.465: 2 0.465 - 0.581: 1 Chirality restraints: 1735 Sorted by residual: chirality pdb=" C1 MAN D 4 " pdb=" O3 BMA D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.66e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.09e+01 chirality pdb=" C1 MAN D 5 " pdb=" O2 MAN D 4 " pdb=" C2 MAN D 5 " pdb=" O5 MAN D 5 " both_signs ideal model delta sigma weight residual False 2.40 2.47 -0.07 2.00e-02 2.50e+03 1.16e+01 ... (remaining 1732 not shown) Planarity restraints: 1871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 435 " 0.052 2.00e-02 2.50e+03 5.18e-02 3.35e+01 pdb=" CG ASN A 435 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 435 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 435 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG A 707 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 202 " 0.047 2.00e-02 2.50e+03 4.03e-02 2.03e+01 pdb=" C7 NAG B 202 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG B 202 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG B 202 " -0.062 2.00e-02 2.50e+03 pdb=" O7 NAG B 202 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 303 " -0.039 2.00e-02 2.50e+03 3.25e-02 1.32e+01 pdb=" C7 NAG C 303 " 0.009 2.00e-02 2.50e+03 pdb=" C8 NAG C 303 " -0.031 2.00e-02 2.50e+03 pdb=" N2 NAG C 303 " 0.052 2.00e-02 2.50e+03 pdb=" O7 NAG C 303 " 0.009 2.00e-02 2.50e+03 ... (remaining 1868 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3371 2.83 - 3.34: 9676 3.34 - 3.86: 18278 3.86 - 4.38: 20796 4.38 - 4.90: 34187 Nonbonded interactions: 86308 Sorted by model distance: nonbonded pdb=" OG1 THR C 200 " pdb=" OE PCA H 1 " model vdw 2.307 2.440 nonbonded pdb=" O3 NAG B 202 " pdb=" O7 NAG B 202 " model vdw 2.361 2.440 nonbonded pdb=" OD1 ASN A 405 " pdb=" OG1 THR A 635 " model vdw 2.412 2.440 nonbonded pdb=" OD1 ASN B 53 " pdb=" O5 NAG B 202 " model vdw 2.416 3.040 nonbonded pdb=" O LEU B 114 " pdb=" OG SER B 117 " model vdw 2.433 2.440 ... (remaining 86303 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 2.930 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.010 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.075 10909 Z= 0.886 Angle : 1.304 22.578 14856 Z= 0.865 Chirality : 0.074 0.581 1735 Planarity : 0.006 0.040 1862 Dihedral : 10.271 78.144 4038 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.40 % Favored : 97.31 % Rotamer: Outliers : 0.43 % Allowed : 1.03 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % 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: 0.06 (0.22), residues: 1336 helix: -0.31 (0.25), residues: 336 sheet: 0.87 (0.29), residues: 307 loop : -0.05 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.006 TRP H 160 HIS 0.006 0.001 HIS A 239 PHE 0.029 0.005 PHE L 101 TYR 0.037 0.005 TYR L 99 ARG 0.007 0.001 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 393 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 398 average time/residue: 0.2345 time to fit residues: 129.9583 Evaluate side-chains 212 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.239 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0994 time to fit residues: 1.8492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS B 30 HIS B 103 HIS ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN L 88 GLN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 ASN L 192 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10909 Z= 0.234 Angle : 0.674 8.402 14856 Z= 0.350 Chirality : 0.045 0.327 1735 Planarity : 0.005 0.041 1862 Dihedral : 6.226 59.698 1669 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.23), residues: 1336 helix: 0.65 (0.27), residues: 335 sheet: 0.84 (0.27), residues: 334 loop : 0.29 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 36 HIS 0.006 0.001 HIS H 206 PHE 0.025 0.003 PHE H 29 TYR 0.028 0.002 TYR H 90 ARG 0.004 0.000 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 279 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.2127 time to fit residues: 85.3317 Evaluate side-chains 191 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 33 optimal weight: 0.3980 chunk 120 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN C 103 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 ASN L 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10909 Z= 0.213 Angle : 0.614 7.606 14856 Z= 0.320 Chirality : 0.043 0.221 1735 Planarity : 0.005 0.047 1862 Dihedral : 5.792 56.182 1669 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % 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: 0.73 (0.23), residues: 1336 helix: 0.86 (0.28), residues: 329 sheet: 0.71 (0.27), residues: 327 loop : 0.32 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 160 HIS 0.007 0.001 HIS A 426 PHE 0.029 0.002 PHE A 649 TYR 0.024 0.002 TYR C 185 ARG 0.011 0.001 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 246 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 248 average time/residue: 0.2008 time to fit residues: 73.5469 Evaluate side-chains 179 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 1.111 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0977 time to fit residues: 1.8963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 0.0670 chunk 128 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 HIS L 174 ASN L 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10909 Z= 0.175 Angle : 0.591 8.452 14856 Z= 0.303 Chirality : 0.044 0.314 1735 Planarity : 0.005 0.041 1862 Dihedral : 5.685 59.709 1669 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % 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: 0.73 (0.23), residues: 1336 helix: 0.73 (0.28), residues: 327 sheet: 0.74 (0.27), residues: 338 loop : 0.37 (0.26), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 189 HIS 0.006 0.001 HIS H 170 PHE 0.024 0.002 PHE C 88 TYR 0.018 0.001 TYR A 404 ARG 0.008 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2492 time to fit residues: 90.4575 Evaluate side-chains 180 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 HIS H 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.069 10909 Z= 0.627 Angle : 1.070 12.844 14856 Z= 0.558 Chirality : 0.054 0.236 1735 Planarity : 0.008 0.093 1862 Dihedral : 7.543 54.958 1669 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 28.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % 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: -0.94 (0.22), residues: 1336 helix: -0.97 (0.25), residues: 334 sheet: 0.04 (0.27), residues: 309 loop : -0.65 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP L 34 HIS 0.015 0.004 HIS A 657 PHE 0.048 0.004 PHE A 298 TYR 0.041 0.004 TYR A 389 ARG 0.021 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.2182 time to fit residues: 58.9381 Evaluate side-chains 130 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 30.0000 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10909 Z= 0.224 Angle : 0.669 12.950 14856 Z= 0.348 Chirality : 0.045 0.276 1735 Planarity : 0.005 0.043 1862 Dihedral : 6.192 55.391 1669 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % 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: -0.08 (0.22), residues: 1336 helix: 0.06 (0.27), residues: 319 sheet: 0.48 (0.28), residues: 305 loop : -0.25 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 189 HIS 0.007 0.001 HIS A 528 PHE 0.023 0.002 PHE A 232 TYR 0.022 0.002 TYR A 658 ARG 0.006 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2125 time to fit residues: 61.5377 Evaluate side-chains 141 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10909 Z= 0.201 Angle : 0.636 9.169 14856 Z= 0.330 Chirality : 0.044 0.204 1735 Planarity : 0.005 0.058 1862 Dihedral : 5.864 54.143 1669 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % 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: 0.14 (0.23), residues: 1336 helix: 0.29 (0.27), residues: 319 sheet: 0.56 (0.27), residues: 312 loop : -0.11 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 125 HIS 0.025 0.001 HIS C 191 PHE 0.020 0.002 PHE C 88 TYR 0.041 0.002 TYR L 49 ARG 0.009 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1993 time to fit residues: 57.5483 Evaluate side-chains 146 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 HIS L 33 HIS L 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10909 Z= 0.179 Angle : 0.615 6.337 14856 Z= 0.316 Chirality : 0.043 0.187 1735 Planarity : 0.005 0.045 1862 Dihedral : 5.803 59.895 1669 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % 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: 0.20 (0.23), residues: 1336 helix: 0.53 (0.27), residues: 314 sheet: 0.43 (0.27), residues: 315 loop : -0.08 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 125 HIS 0.007 0.001 HIS H 170 PHE 0.029 0.002 PHE A 238 TYR 0.016 0.001 TYR H 108 ARG 0.006 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2179 time to fit residues: 62.6876 Evaluate side-chains 146 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.4980 chunk 122 optimal weight: 6.9990 chunk 112 optimal weight: 0.0970 chunk 119 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 ASN L 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10909 Z= 0.194 Angle : 0.613 7.306 14856 Z= 0.314 Chirality : 0.043 0.191 1735 Planarity : 0.005 0.044 1862 Dihedral : 5.594 54.112 1669 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % 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: 0.19 (0.23), residues: 1336 helix: 0.55 (0.28), residues: 313 sheet: 0.42 (0.27), residues: 310 loop : -0.10 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 125 HIS 0.008 0.001 HIS A 303 PHE 0.027 0.002 PHE A 298 TYR 0.017 0.002 TYR H 108 ARG 0.006 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1949 time to fit residues: 55.5508 Evaluate side-chains 149 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10909 Z= 0.178 Angle : 0.616 7.307 14856 Z= 0.314 Chirality : 0.043 0.189 1735 Planarity : 0.005 0.044 1862 Dihedral : 5.550 54.936 1669 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % 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: 0.23 (0.23), residues: 1336 helix: 0.60 (0.28), residues: 312 sheet: 0.46 (0.27), residues: 312 loop : -0.09 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 125 HIS 0.005 0.001 HIS A 303 PHE 0.022 0.002 PHE B 88 TYR 0.026 0.002 TYR C 101 ARG 0.012 0.001 ARG H 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2007 time to fit residues: 55.8311 Evaluate side-chains 142 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 HIS L 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.053789 restraints weight = 48274.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.055682 restraints weight = 27815.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.056972 restraints weight = 18660.621| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10909 Z= 0.178 Angle : 0.606 8.427 14856 Z= 0.309 Chirality : 0.043 0.211 1735 Planarity : 0.005 0.055 1862 Dihedral : 5.421 54.351 1669 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % 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: 0.22 (0.23), residues: 1336 helix: 0.52 (0.28), residues: 314 sheet: 0.49 (0.27), residues: 315 loop : -0.09 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 125 HIS 0.007 0.001 HIS H 170 PHE 0.016 0.002 PHE B 89 TYR 0.018 0.001 TYR C 101 ARG 0.006 0.000 ARG H 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2376.55 seconds wall clock time: 44 minutes 23.61 seconds (2663.61 seconds total)