Starting phenix.real_space_refine on Fri Mar 15 05:11:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/03_2024/6c5v_7344_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/03_2024/6c5v_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_7344/03_2024/6c5v_7344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/03_2024/6c5v_7344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/03_2024/6c5v_7344_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/03_2024/6c5v_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-dev-5265/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: 18 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: 5.90, per 1000 atoms: 0.55 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: 4.44 Conformation dependent library (CDL) restraints added in 1.9 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: 2.19 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: 3.17 Time building geometry restraints manager: 4.87 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 - 21.48: 6461 21.48 - 42.95: 138 42.95 - 64.43: 53 64.43 - 85.91: 13 85.91 - 107.38: 5 Dihedral angle restraints: 6670 sinusoidal: 2751 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=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.67 107.38 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 6667 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.850 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 31.590 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.850 ------------------------------------------------------------------------------- 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 : 11.190 107.382 4114 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 : 1.225 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 REVERT: A 25 LEU cc_start: 0.8735 (tt) cc_final: 0.8475 (mp) REVERT: A 73 LYS cc_start: 0.9077 (pttt) cc_final: 0.8853 (ttpt) REVERT: A 137 MET cc_start: 0.8720 (tpt) cc_final: 0.8476 (tmm) REVERT: A 217 THR cc_start: 0.9416 (m) cc_final: 0.9054 (t) REVERT: A 283 LEU cc_start: 0.9224 (mt) cc_final: 0.8974 (mt) REVERT: A 286 GLU cc_start: 0.8477 (tt0) cc_final: 0.8257 (tm-30) REVERT: A 317 TRP cc_start: 0.9231 (t60) cc_final: 0.8607 (t60) REVERT: A 318 LEU cc_start: 0.9669 (mt) cc_final: 0.9264 (mt) REVERT: A 384 PRO cc_start: 0.8738 (Cg_endo) cc_final: 0.8311 (Cg_exo) REVERT: A 404 TYR cc_start: 0.8521 (t80) cc_final: 0.8318 (t80) REVERT: A 413 LEU cc_start: 0.9196 (mt) cc_final: 0.8803 (tp) REVERT: A 417 MET cc_start: 0.8654 (mtt) cc_final: 0.8027 (mmm) REVERT: A 466 LEU cc_start: 0.8762 (mt) cc_final: 0.8534 (tt) REVERT: A 537 ARG cc_start: 0.8321 (mmt-90) cc_final: 0.8083 (mtt180) REVERT: A 551 THR cc_start: 0.9436 (m) cc_final: 0.8891 (p) REVERT: A 582 VAL cc_start: 0.9275 (t) cc_final: 0.8977 (t) REVERT: A 614 PHE cc_start: 0.8703 (m-80) cc_final: 0.8141 (m-80) REVERT: B 81 ASN cc_start: 0.8692 (t0) cc_final: 0.7772 (p0) REVERT: B 84 ASN cc_start: 0.9456 (m-40) cc_final: 0.9100 (m-40) REVERT: B 89 PHE cc_start: 0.9082 (m-80) cc_final: 0.8544 (m-80) REVERT: B 106 GLU cc_start: 0.9335 (tt0) cc_final: 0.8836 (tm-30) REVERT: B 115 TYR cc_start: 0.7975 (t80) cc_final: 0.7448 (t80) REVERT: B 128 LEU cc_start: 0.8441 (mt) cc_final: 0.8127 (mm) REVERT: C 81 TRP cc_start: 0.8456 (m-90) cc_final: 0.8210 (m100) REVERT: C 98 ASN cc_start: 0.0921 (OUTLIER) cc_final: -0.0613 (t0) REVERT: C 116 PHE cc_start: 0.8122 (m-80) cc_final: 0.7467 (m-80) REVERT: C 155 ASN cc_start: 0.7223 (m-40) cc_final: 0.7002 (m-40) REVERT: C 169 VAL cc_start: 0.7855 (t) cc_final: 0.7646 (p) REVERT: C 171 GLU cc_start: 0.8326 (mm-30) cc_final: 0.6783 (tm-30) REVERT: C 182 PHE cc_start: 0.7768 (m-80) cc_final: 0.7554 (m-80) REVERT: C 188 PHE cc_start: 0.8755 (m-80) cc_final: 0.8509 (m-80) REVERT: C 211 LEU cc_start: 0.9069 (mt) cc_final: 0.8585 (mm) REVERT: H 25 SER cc_start: 0.7949 (t) cc_final: 0.7677 (m) REVERT: H 32 PHE cc_start: 0.8798 (m-80) cc_final: 0.8303 (m-80) REVERT: H 69 MET cc_start: 0.7626 (mtm) cc_final: 0.6946 (mtm) REVERT: H 98 MET cc_start: 0.8100 (ttt) cc_final: 0.5716 (tpt) REVERT: H 160 TRP cc_start: 0.8302 (m100) cc_final: 0.7948 (m100) REVERT: H 165 LEU cc_start: 0.8342 (tp) cc_final: 0.7845 (mm) REVERT: H 215 LYS cc_start: 0.7945 (tppt) cc_final: 0.7733 (tptp) REVERT: L 3 GLU cc_start: 0.8691 (tt0) cc_final: 0.8275 (tm-30) REVERT: L 4 LEU cc_start: 0.8856 (mt) cc_final: 0.8630 (tt) REVERT: L 20 ILE cc_start: 0.9481 (mm) cc_final: 0.9275 (tp) REVERT: L 49 TYR cc_start: 0.8794 (m-80) cc_final: 0.7943 (m-80) REVERT: L 75 SER cc_start: 0.8572 (t) cc_final: 0.7781 (m) REVERT: L 84 ASP cc_start: 0.8821 (m-30) cc_final: 0.8545 (m-30) REVERT: L 99 TYR cc_start: 0.7893 (m-80) cc_final: 0.7300 (m-80) REVERT: L 121 LEU cc_start: 0.8511 (tp) cc_final: 0.8203 (tt) REVERT: L 136 LEU cc_start: 0.8919 (mt) cc_final: 0.8570 (mm) REVERT: L 138 CYS cc_start: 0.7638 (t) cc_final: 0.6899 (t) REVERT: L 143 PHE cc_start: 0.8874 (p90) cc_final: 0.8357 (p90) REVERT: L 174 ASN cc_start: 0.8797 (t0) cc_final: 0.8476 (t0) outliers start: 5 outliers final: 1 residues processed: 398 average time/residue: 0.2286 time to fit residues: 126.3453 Evaluate side-chains 236 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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: 4.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS B 103 HIS ** C 103 ASN ** 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 36 GLN L 88 GLN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10909 Z= 0.237 Angle : 0.639 7.482 14856 Z= 0.343 Chirality : 0.043 0.246 1735 Planarity : 0.005 0.041 1862 Dihedral : 8.228 85.539 1745 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: 0.75 (0.23), residues: 1336 helix: 0.79 (0.27), residues: 335 sheet: 0.99 (0.28), residues: 323 loop : 0.23 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.006 0.001 HIS H 206 PHE 0.024 0.003 PHE L 101 TYR 0.027 0.002 TYR C 185 ARG 0.005 0.000 ARG A 418 *********************** 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 286 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.217 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: A 103 ASP cc_start: 0.8370 (t0) cc_final: 0.8069 (t0) REVERT: A 137 MET cc_start: 0.8568 (tpt) cc_final: 0.8296 (tpp) REVERT: A 138 LEU cc_start: 0.9341 (mt) cc_final: 0.9028 (mt) REVERT: A 217 THR cc_start: 0.9359 (m) cc_final: 0.9141 (t) REVERT: A 256 MET cc_start: 0.9394 (tpt) cc_final: 0.8436 (tpp) REVERT: A 283 LEU cc_start: 0.9217 (mt) cc_final: 0.8862 (mt) REVERT: A 286 GLU cc_start: 0.8608 (tt0) cc_final: 0.8330 (tm-30) REVERT: A 317 TRP cc_start: 0.9086 (t60) cc_final: 0.8450 (t60) REVERT: A 318 LEU cc_start: 0.9642 (mt) cc_final: 0.9360 (mt) REVERT: A 349 GLU cc_start: 0.9272 (tt0) cc_final: 0.8943 (tt0) REVERT: A 413 LEU cc_start: 0.8945 (mt) cc_final: 0.8612 (tp) REVERT: A 417 MET cc_start: 0.8611 (mtt) cc_final: 0.8184 (mmm) REVERT: A 458 GLU cc_start: 0.8740 (tt0) cc_final: 0.7887 (tt0) REVERT: A 494 MET cc_start: 0.8060 (ttm) cc_final: 0.7729 (ttm) REVERT: A 537 ARG cc_start: 0.8330 (mmt-90) cc_final: 0.8051 (mtt180) REVERT: A 614 PHE cc_start: 0.8639 (m-80) cc_final: 0.8167 (m-80) REVERT: A 649 PHE cc_start: 0.8550 (m-80) cc_final: 0.8164 (m-80) REVERT: A 661 LEU cc_start: 0.8842 (mt) cc_final: 0.8638 (mp) REVERT: B 81 ASN cc_start: 0.8880 (t0) cc_final: 0.8451 (t0) REVERT: B 84 ASN cc_start: 0.9355 (m-40) cc_final: 0.9041 (m-40) REVERT: B 89 PHE cc_start: 0.9137 (m-80) cc_final: 0.8266 (m-80) REVERT: B 106 GLU cc_start: 0.9327 (tt0) cc_final: 0.8874 (tm-30) REVERT: B 112 GLU cc_start: 0.9203 (pt0) cc_final: 0.8951 (pt0) REVERT: B 128 LEU cc_start: 0.8319 (mt) cc_final: 0.7910 (mm) REVERT: C 73 ASP cc_start: 0.6894 (t0) cc_final: 0.6254 (t0) REVERT: C 81 TRP cc_start: 0.8656 (m-90) cc_final: 0.8196 (m100) REVERT: C 116 PHE cc_start: 0.8381 (m-80) cc_final: 0.7580 (m-80) REVERT: C 155 ASN cc_start: 0.7206 (m-40) cc_final: 0.6975 (m110) REVERT: C 171 GLU cc_start: 0.8081 (mm-30) cc_final: 0.6808 (tm-30) REVERT: C 182 PHE cc_start: 0.8194 (m-80) cc_final: 0.7566 (m-80) REVERT: C 198 PHE cc_start: 0.9016 (m-10) cc_final: 0.8787 (m-10) REVERT: H 32 PHE cc_start: 0.8847 (m-80) cc_final: 0.8250 (m-80) REVERT: H 90 TYR cc_start: 0.8296 (m-80) cc_final: 0.7937 (m-10) REVERT: H 97 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6321 (tm-30) REVERT: H 98 MET cc_start: 0.6918 (ttt) cc_final: 0.6098 (tpt) REVERT: H 101 ARG cc_start: 0.8646 (ptp-170) cc_final: 0.8168 (ptp-170) REVERT: L 3 GLU cc_start: 0.8683 (tt0) cc_final: 0.8421 (tm-30) REVERT: L 4 LEU cc_start: 0.8772 (mt) cc_final: 0.8521 (tp) REVERT: L 20 ILE cc_start: 0.9393 (mm) cc_final: 0.9162 (pt) REVERT: L 57 ILE cc_start: 0.7792 (mp) cc_final: 0.7326 (mp) REVERT: L 84 ASP cc_start: 0.8832 (m-30) cc_final: 0.8557 (m-30) REVERT: L 99 TYR cc_start: 0.7935 (m-80) cc_final: 0.6939 (m-80) REVERT: L 128 GLU cc_start: 0.9357 (tp30) cc_final: 0.8960 (tp30) REVERT: L 136 LEU cc_start: 0.8866 (mt) cc_final: 0.8578 (mm) REVERT: L 143 PHE cc_start: 0.8922 (p90) cc_final: 0.8236 (p90) REVERT: L 174 ASN cc_start: 0.8565 (t0) cc_final: 0.8118 (t0) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2151 time to fit residues: 87.3702 Evaluate side-chains 212 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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: 8.9990 chunk 37 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 119 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 10909 Z= 0.443 Angle : 0.806 11.201 14856 Z= 0.420 Chirality : 0.046 0.191 1735 Planarity : 0.006 0.060 1862 Dihedral : 8.160 80.237 1745 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.07 % 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: 0.13 (0.26), residues: 341 sheet: 0.71 (0.27), residues: 323 loop : -0.21 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 125 HIS 0.010 0.003 HIS A 407 PHE 0.028 0.003 PHE B 89 TYR 0.025 0.003 TYR A 389 ARG 0.037 0.001 ARG L 17 *********************** 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 221 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 1.252 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: A 160 LEU cc_start: 0.9012 (pt) cc_final: 0.8240 (tp) REVERT: A 286 GLU cc_start: 0.8650 (tt0) cc_final: 0.8192 (tm-30) REVERT: A 317 TRP cc_start: 0.9265 (t60) cc_final: 0.8604 (t60) REVERT: A 318 LEU cc_start: 0.9778 (mt) cc_final: 0.9396 (mt) REVERT: A 349 GLU cc_start: 0.9372 (tt0) cc_final: 0.8988 (tt0) REVERT: A 413 LEU cc_start: 0.8971 (mt) cc_final: 0.8578 (tp) REVERT: A 417 MET cc_start: 0.8751 (mtt) cc_final: 0.8542 (mpp) REVERT: A 458 GLU cc_start: 0.8896 (tt0) cc_final: 0.8018 (tt0) REVERT: A 537 ARG cc_start: 0.8506 (mmt-90) cc_final: 0.8148 (mtt180) REVERT: A 544 ILE cc_start: 0.9361 (mt) cc_final: 0.8819 (mt) REVERT: A 614 PHE cc_start: 0.8734 (m-80) cc_final: 0.8192 (m-80) REVERT: A 649 PHE cc_start: 0.8671 (m-80) cc_final: 0.8463 (m-80) REVERT: B 30 HIS cc_start: 0.6911 (t70) cc_final: 0.6111 (t70) REVERT: B 89 PHE cc_start: 0.9238 (m-80) cc_final: 0.8705 (m-80) REVERT: B 100 LEU cc_start: 0.9261 (mt) cc_final: 0.9005 (mt) REVERT: B 106 GLU cc_start: 0.9470 (tt0) cc_final: 0.8835 (tm-30) REVERT: B 112 GLU cc_start: 0.9330 (pt0) cc_final: 0.8875 (pt0) REVERT: C 81 TRP cc_start: 0.9013 (m-90) cc_final: 0.8113 (m100) REVERT: C 116 PHE cc_start: 0.8482 (m-80) cc_final: 0.7642 (m-80) REVERT: C 171 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7082 (tm-30) REVERT: C 198 PHE cc_start: 0.9107 (m-10) cc_final: 0.8846 (m-10) REVERT: H 52 ASP cc_start: 0.9255 (t70) cc_final: 0.8422 (p0) REVERT: H 64 GLN cc_start: 0.8506 (tp40) cc_final: 0.8174 (pp30) REVERT: H 80 MET cc_start: 0.8755 (tmm) cc_final: 0.8456 (tmm) REVERT: H 90 TYR cc_start: 0.8507 (m-80) cc_final: 0.8073 (m-10) REVERT: H 97 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7544 (tm-30) REVERT: H 98 MET cc_start: 0.7820 (ttt) cc_final: 0.6818 (tpt) REVERT: L 3 GLU cc_start: 0.8825 (tt0) cc_final: 0.8554 (tm-30) REVERT: L 4 LEU cc_start: 0.8761 (mt) cc_final: 0.8480 (mm) REVERT: L 99 TYR cc_start: 0.8740 (m-80) cc_final: 0.6681 (m-80) REVERT: L 136 LEU cc_start: 0.8855 (mt) cc_final: 0.8436 (mm) REVERT: L 143 PHE cc_start: 0.9030 (p90) cc_final: 0.8243 (p90) outliers start: 1 outliers final: 1 residues processed: 221 average time/residue: 0.1968 time to fit residues: 64.2433 Evaluate side-chains 172 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** 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: 0.8231 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10909 Z= 0.266 Angle : 0.644 7.828 14856 Z= 0.335 Chirality : 0.043 0.179 1735 Planarity : 0.005 0.045 1862 Dihedral : 7.618 72.315 1745 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 0.31 (0.26), residues: 343 sheet: 0.69 (0.27), residues: 318 loop : -0.07 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 160 HIS 0.006 0.001 HIS A 528 PHE 0.025 0.002 PHE C 88 TYR 0.020 0.002 TYR B 115 ARG 0.008 0.001 ARG L 17 *********************** 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 221 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.246 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: A 160 LEU cc_start: 0.8828 (pt) cc_final: 0.8174 (tp) REVERT: A 249 MET cc_start: 0.8848 (tpp) cc_final: 0.8635 (tpp) REVERT: A 256 MET cc_start: 0.9162 (tpp) cc_final: 0.8505 (tpp) REVERT: A 286 GLU cc_start: 0.8572 (tt0) cc_final: 0.8315 (tm-30) REVERT: A 317 TRP cc_start: 0.9259 (t60) cc_final: 0.8675 (t60) REVERT: A 318 LEU cc_start: 0.9775 (mt) cc_final: 0.9500 (mt) REVERT: A 349 GLU cc_start: 0.9326 (tt0) cc_final: 0.8892 (tt0) REVERT: A 413 LEU cc_start: 0.8991 (mt) cc_final: 0.8597 (tp) REVERT: A 417 MET cc_start: 0.8795 (mtt) cc_final: 0.8530 (mpp) REVERT: A 458 GLU cc_start: 0.8926 (tt0) cc_final: 0.8020 (tt0) REVERT: A 482 LEU cc_start: 0.9354 (mt) cc_final: 0.9118 (mt) REVERT: A 494 MET cc_start: 0.8410 (ttm) cc_final: 0.8193 (ttm) REVERT: A 537 ARG cc_start: 0.8387 (mmt-90) cc_final: 0.8083 (mtt180) REVERT: A 544 ILE cc_start: 0.9302 (mt) cc_final: 0.9087 (mt) REVERT: A 614 PHE cc_start: 0.8750 (m-80) cc_final: 0.8211 (m-80) REVERT: A 649 PHE cc_start: 0.8568 (m-80) cc_final: 0.8284 (m-80) REVERT: B 81 ASN cc_start: 0.8782 (t0) cc_final: 0.8467 (t0) REVERT: B 89 PHE cc_start: 0.9142 (m-80) cc_final: 0.8592 (m-80) REVERT: B 100 LEU cc_start: 0.9273 (mt) cc_final: 0.9014 (mt) REVERT: B 106 GLU cc_start: 0.9370 (tt0) cc_final: 0.8816 (tm-30) REVERT: B 107 LEU cc_start: 0.9537 (tp) cc_final: 0.9314 (tp) REVERT: B 112 GLU cc_start: 0.9305 (pt0) cc_final: 0.9010 (pt0) REVERT: C 73 ASP cc_start: 0.8200 (t0) cc_final: 0.7996 (t0) REVERT: C 81 TRP cc_start: 0.8938 (m-90) cc_final: 0.8065 (m100) REVERT: C 105 ARG cc_start: 0.9422 (tpp80) cc_final: 0.9136 (tpp80) REVERT: C 116 PHE cc_start: 0.8436 (m-80) cc_final: 0.7526 (m-80) REVERT: C 171 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7047 (tm-30) REVERT: H 34 ILE cc_start: 0.8624 (mt) cc_final: 0.8404 (mt) REVERT: H 90 TYR cc_start: 0.8488 (m-80) cc_final: 0.7736 (m-10) REVERT: H 97 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6440 (tm-30) REVERT: H 98 MET cc_start: 0.7765 (ttt) cc_final: 0.6865 (tpt) REVERT: L 3 GLU cc_start: 0.8781 (tt0) cc_final: 0.8373 (tm-30) REVERT: L 4 LEU cc_start: 0.8768 (mt) cc_final: 0.8341 (tp) REVERT: L 99 TYR cc_start: 0.8538 (m-80) cc_final: 0.6510 (m-80) REVERT: L 128 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8826 (tp30) REVERT: L 136 LEU cc_start: 0.8832 (mt) cc_final: 0.8429 (mm) REVERT: L 143 PHE cc_start: 0.9008 (p90) cc_final: 0.8300 (p90) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1997 time to fit residues: 64.6740 Evaluate side-chains 166 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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: 3.9990 chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 0.0050 chunk 115 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 30 HIS ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4654 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= 0.225 Angle : 0.625 12.474 14856 Z= 0.322 Chirality : 0.043 0.188 1735 Planarity : 0.005 0.044 1862 Dihedral : 7.143 63.991 1745 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 0.33 (0.23), residues: 1336 helix: 0.63 (0.27), residues: 338 sheet: 0.68 (0.28), residues: 308 loop : -0.10 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 189 HIS 0.006 0.001 HIS A 239 PHE 0.020 0.002 PHE A 238 TYR 0.018 0.002 TYR A 479 ARG 0.010 0.001 ARG A 430 *********************** 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 222 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.149 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: A 226 LEU cc_start: 0.8182 (mt) cc_final: 0.7891 (mt) REVERT: A 256 MET cc_start: 0.9166 (tpp) cc_final: 0.8548 (tpp) REVERT: A 286 GLU cc_start: 0.8456 (tt0) cc_final: 0.8154 (tm-30) REVERT: A 317 TRP cc_start: 0.9232 (t60) cc_final: 0.8663 (t60) REVERT: A 318 LEU cc_start: 0.9759 (mt) cc_final: 0.9474 (mt) REVERT: A 349 GLU cc_start: 0.9246 (tt0) cc_final: 0.8805 (tt0) REVERT: A 413 LEU cc_start: 0.8981 (mt) cc_final: 0.8608 (tp) REVERT: A 458 GLU cc_start: 0.8851 (tt0) cc_final: 0.8033 (tt0) REVERT: A 494 MET cc_start: 0.8351 (ttm) cc_final: 0.8117 (ttm) REVERT: A 517 LEU cc_start: 0.9412 (mp) cc_final: 0.9164 (mt) REVERT: A 537 ARG cc_start: 0.8196 (mmt-90) cc_final: 0.7174 (mmm160) REVERT: A 544 ILE cc_start: 0.9302 (mt) cc_final: 0.9089 (mt) REVERT: A 614 PHE cc_start: 0.8781 (m-80) cc_final: 0.8226 (m-80) REVERT: A 649 PHE cc_start: 0.8527 (m-80) cc_final: 0.8136 (m-80) REVERT: B 81 ASN cc_start: 0.8725 (t0) cc_final: 0.8479 (t0) REVERT: B 89 PHE cc_start: 0.9068 (m-80) cc_final: 0.8492 (m-80) REVERT: B 106 GLU cc_start: 0.9369 (tt0) cc_final: 0.8792 (tm-30) REVERT: B 107 LEU cc_start: 0.9514 (tp) cc_final: 0.9283 (tp) REVERT: C 81 TRP cc_start: 0.8823 (m-90) cc_final: 0.7916 (m100) REVERT: C 92 GLN cc_start: 0.9250 (mm110) cc_final: 0.9028 (mm110) REVERT: C 105 ARG cc_start: 0.9430 (tpp80) cc_final: 0.9131 (tpp80) REVERT: C 116 PHE cc_start: 0.8436 (m-80) cc_final: 0.7503 (m-80) REVERT: C 171 GLU cc_start: 0.7855 (mm-30) cc_final: 0.6988 (tm-30) REVERT: H 34 ILE cc_start: 0.8711 (mt) cc_final: 0.8502 (mt) REVERT: H 90 TYR cc_start: 0.8686 (m-80) cc_final: 0.7878 (m-10) REVERT: H 97 GLU cc_start: 0.6767 (tm-30) cc_final: 0.6308 (tm-30) REVERT: H 98 MET cc_start: 0.7453 (ttt) cc_final: 0.6444 (tpt) REVERT: H 212 LYS cc_start: 0.9134 (tttp) cc_final: 0.8741 (tmtt) REVERT: L 3 GLU cc_start: 0.8743 (tt0) cc_final: 0.8292 (tm-30) REVERT: L 4 LEU cc_start: 0.8774 (mt) cc_final: 0.8346 (tp) REVERT: L 99 TYR cc_start: 0.8398 (m-80) cc_final: 0.6522 (m-80) REVERT: L 128 GLU cc_start: 0.9304 (mm-30) cc_final: 0.9092 (tp30) REVERT: L 136 LEU cc_start: 0.8604 (mt) cc_final: 0.8317 (mp) REVERT: L 143 PHE cc_start: 0.8967 (p90) cc_final: 0.8374 (p90) REVERT: L 182 LEU cc_start: 0.8863 (tt) cc_final: 0.8622 (tt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2013 time to fit residues: 65.4327 Evaluate side-chains 172 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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: 6.9990 chunk 115 optimal weight: 0.7980 chunk 25 optimal weight: 0.0570 chunk 75 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS C 103 ASN H 53 ASN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN L 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10909 Z= 0.174 Angle : 0.597 12.010 14856 Z= 0.304 Chirality : 0.044 0.301 1735 Planarity : 0.005 0.047 1862 Dihedral : 6.580 57.138 1745 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.09 % Allowed : 1.29 % Favored : 98.62 % 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: 0.55 (0.23), residues: 1336 helix: 0.96 (0.28), residues: 336 sheet: 0.68 (0.28), residues: 309 loop : 0.02 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 160 HIS 0.008 0.001 HIS A 239 PHE 0.014 0.002 PHE C 198 TYR 0.019 0.001 TYR H 90 ARG 0.005 0.000 ARG A 430 *********************** 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 226 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 1.229 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: A 226 LEU cc_start: 0.8188 (mt) cc_final: 0.7936 (mt) REVERT: A 256 MET cc_start: 0.9147 (tpp) cc_final: 0.8469 (tpp) REVERT: A 317 TRP cc_start: 0.9185 (t60) cc_final: 0.8682 (t60) REVERT: A 318 LEU cc_start: 0.9764 (mt) cc_final: 0.9481 (pp) REVERT: A 349 GLU cc_start: 0.9254 (tt0) cc_final: 0.8802 (tt0) REVERT: A 417 MET cc_start: 0.9023 (mpp) cc_final: 0.8301 (ptp) REVERT: A 458 GLU cc_start: 0.8985 (tt0) cc_final: 0.8430 (tt0) REVERT: A 537 ARG cc_start: 0.8176 (mmt-90) cc_final: 0.7949 (mtt180) REVERT: A 543 MET cc_start: 0.8521 (tpp) cc_final: 0.8263 (tpp) REVERT: A 614 PHE cc_start: 0.8785 (m-80) cc_final: 0.8252 (m-80) REVERT: A 649 PHE cc_start: 0.8370 (m-80) cc_final: 0.8162 (m-80) REVERT: B 89 PHE cc_start: 0.9045 (m-80) cc_final: 0.8425 (m-80) REVERT: B 106 GLU cc_start: 0.9353 (tt0) cc_final: 0.8856 (pt0) REVERT: C 73 ASP cc_start: 0.8203 (t0) cc_final: 0.7960 (t0) REVERT: C 81 TRP cc_start: 0.8751 (m-90) cc_final: 0.7844 (m100) REVERT: C 92 GLN cc_start: 0.9265 (mm110) cc_final: 0.9030 (mm110) REVERT: C 105 ARG cc_start: 0.9389 (tpp80) cc_final: 0.9075 (tpp80) REVERT: C 106 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8117 (mt-10) REVERT: C 116 PHE cc_start: 0.8061 (m-80) cc_final: 0.7094 (m-80) REVERT: C 117 TYR cc_start: 0.8680 (m-10) cc_final: 0.8337 (m-10) REVERT: C 171 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7008 (tm-30) REVERT: H 34 ILE cc_start: 0.8812 (mt) cc_final: 0.8601 (mt) REVERT: H 90 TYR cc_start: 0.8600 (m-10) cc_final: 0.7818 (m-10) REVERT: H 98 MET cc_start: 0.7428 (ttt) cc_final: 0.6699 (tpt) REVERT: H 212 LYS cc_start: 0.9131 (tttp) cc_final: 0.8233 (mmtt) REVERT: H 215 LYS cc_start: 0.8260 (ttmm) cc_final: 0.7557 (tptp) REVERT: L 3 GLU cc_start: 0.8747 (tt0) cc_final: 0.8311 (tm-30) REVERT: L 4 LEU cc_start: 0.8765 (mt) cc_final: 0.8306 (tp) REVERT: L 99 TYR cc_start: 0.8264 (m-80) cc_final: 0.6367 (m-80) REVERT: L 128 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9120 (tp30) REVERT: L 143 PHE cc_start: 0.8905 (p90) cc_final: 0.8363 (p90) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.2087 time to fit residues: 68.0321 Evaluate side-chains 170 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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: 0.7980 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 655 HIS A 657 HIS B 30 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 10909 Z= 0.414 Angle : 0.786 12.260 14856 Z= 0.405 Chirality : 0.046 0.213 1735 Planarity : 0.006 0.062 1862 Dihedral : 7.119 55.414 1745 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % 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: -0.13 (0.22), residues: 1336 helix: 0.29 (0.27), residues: 326 sheet: 0.38 (0.27), residues: 312 loop : -0.41 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP H 36 HIS 0.012 0.002 HIS A 528 PHE 0.030 0.003 PHE B 89 TYR 0.025 0.003 TYR A 389 ARG 0.013 0.001 ARG A 418 *********************** 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 199 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.127 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: A 91 ASP cc_start: 0.8061 (p0) cc_final: 0.7779 (p0) REVERT: A 349 GLU cc_start: 0.9405 (tt0) cc_final: 0.9061 (tt0) REVERT: A 458 GLU cc_start: 0.8774 (tt0) cc_final: 0.8004 (tt0) REVERT: A 544 ILE cc_start: 0.9253 (mt) cc_final: 0.9045 (mt) REVERT: A 578 PHE cc_start: 0.6822 (m-80) cc_final: 0.6559 (m-80) REVERT: A 649 PHE cc_start: 0.8686 (m-80) cc_final: 0.8421 (m-80) REVERT: B 89 PHE cc_start: 0.9262 (m-80) cc_final: 0.8742 (m-80) REVERT: C 73 ASP cc_start: 0.8572 (t0) cc_final: 0.8266 (t0) REVERT: C 92 GLN cc_start: 0.9285 (mm110) cc_final: 0.8820 (pp30) REVERT: C 105 ARG cc_start: 0.9430 (tpp80) cc_final: 0.9152 (tpp80) REVERT: C 116 PHE cc_start: 0.8310 (m-80) cc_final: 0.7282 (m-80) REVERT: C 117 TYR cc_start: 0.8942 (m-10) cc_final: 0.8615 (m-10) REVERT: C 125 TRP cc_start: 0.8355 (t60) cc_final: 0.7326 (t60) REVERT: C 171 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7000 (tm-30) REVERT: H 98 MET cc_start: 0.7950 (ttt) cc_final: 0.7230 (tpt) REVERT: H 104 PHE cc_start: 0.9258 (m-80) cc_final: 0.8197 (m-80) REVERT: H 215 LYS cc_start: 0.7783 (ttmm) cc_final: 0.7325 (tptp) REVERT: L 27 ILE cc_start: 0.9207 (tp) cc_final: 0.8998 (tp) REVERT: L 99 TYR cc_start: 0.8547 (m-80) cc_final: 0.6599 (m-80) REVERT: L 143 PHE cc_start: 0.8868 (p90) cc_final: 0.8286 (p90) REVERT: L 197 CYS cc_start: 0.7399 (t) cc_final: 0.6703 (p) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1910 time to fit residues: 56.2586 Evaluate side-chains 150 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 81 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** H 61 GLN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5447 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= 0.176 Angle : 0.615 9.440 14856 Z= 0.313 Chirality : 0.043 0.210 1735 Planarity : 0.005 0.050 1862 Dihedral : 6.338 59.408 1745 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 0.29 (0.23), residues: 1336 helix: 0.69 (0.28), residues: 327 sheet: 0.52 (0.27), residues: 318 loop : -0.11 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 160 HIS 0.009 0.001 HIS A 426 PHE 0.022 0.002 PHE A 232 TYR 0.033 0.002 TYR L 49 ARG 0.004 0.000 ARG A 430 *********************** 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 220 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.000 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: A 68 MET cc_start: 0.8442 (tpp) cc_final: 0.8142 (mmm) REVERT: A 160 LEU cc_start: 0.8927 (pt) cc_final: 0.8151 (tp) REVERT: A 226 LEU cc_start: 0.8201 (mt) cc_final: 0.7981 (mt) REVERT: A 256 MET cc_start: 0.9407 (tpt) cc_final: 0.8596 (tpt) REVERT: A 317 TRP cc_start: 0.9237 (t60) cc_final: 0.8741 (t60) REVERT: A 318 LEU cc_start: 0.9769 (mt) cc_final: 0.9504 (pp) REVERT: A 349 GLU cc_start: 0.9276 (tt0) cc_final: 0.8805 (tt0) REVERT: A 356 MET cc_start: 0.8764 (tpp) cc_final: 0.8538 (tpp) REVERT: A 458 GLU cc_start: 0.8980 (tt0) cc_final: 0.8435 (tt0) REVERT: A 494 MET cc_start: 0.8410 (ttm) cc_final: 0.8158 (ttm) REVERT: A 543 MET cc_start: 0.8363 (tpp) cc_final: 0.8071 (tpp) REVERT: A 649 PHE cc_start: 0.8580 (m-80) cc_final: 0.8262 (m-80) REVERT: A 668 MET cc_start: 0.8455 (mpp) cc_final: 0.8237 (mpp) REVERT: B 89 PHE cc_start: 0.9030 (m-80) cc_final: 0.8451 (m-80) REVERT: B 106 GLU cc_start: 0.9308 (tt0) cc_final: 0.8758 (pt0) REVERT: C 65 LYS cc_start: 0.8314 (tttt) cc_final: 0.7592 (tmtt) REVERT: C 73 ASP cc_start: 0.8513 (t0) cc_final: 0.8172 (t0) REVERT: C 81 TRP cc_start: 0.8673 (m-90) cc_final: 0.7854 (m100) REVERT: C 92 GLN cc_start: 0.9223 (mm110) cc_final: 0.8685 (pp30) REVERT: C 105 ARG cc_start: 0.9398 (tpp80) cc_final: 0.9126 (tpp80) REVERT: C 116 PHE cc_start: 0.8146 (m-80) cc_final: 0.7094 (m-80) REVERT: C 117 TYR cc_start: 0.8916 (m-10) cc_final: 0.8517 (m-10) REVERT: C 171 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7071 (tm-30) REVERT: H 98 MET cc_start: 0.6780 (ttt) cc_final: 0.6380 (tpt) REVERT: H 212 LYS cc_start: 0.9200 (tttm) cc_final: 0.8474 (mmtt) REVERT: H 215 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7614 (tptp) REVERT: L 3 GLU cc_start: 0.8843 (tt0) cc_final: 0.8346 (tm-30) REVERT: L 4 LEU cc_start: 0.8598 (mm) cc_final: 0.8245 (tp) REVERT: L 86 TYR cc_start: 0.8453 (m-80) cc_final: 0.7928 (m-10) REVERT: L 99 TYR cc_start: 0.8223 (m-80) cc_final: 0.6229 (m-80) REVERT: L 136 LEU cc_start: 0.8653 (mm) cc_final: 0.8321 (mp) REVERT: L 143 PHE cc_start: 0.8801 (p90) cc_final: 0.8300 (p90) REVERT: L 197 CYS cc_start: 0.7162 (t) cc_final: 0.6499 (p) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2043 time to fit residues: 65.0706 Evaluate side-chains 167 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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: 0.3980 chunk 122 optimal weight: 0.5980 chunk 112 optimal weight: 0.0000 chunk 119 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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** B 30 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS L 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10909 Z= 0.159 Angle : 0.589 10.090 14856 Z= 0.298 Chirality : 0.043 0.200 1735 Planarity : 0.005 0.044 1862 Dihedral : 5.916 55.663 1745 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 0.46 (0.23), residues: 1336 helix: 0.83 (0.28), residues: 319 sheet: 0.61 (0.27), residues: 314 loop : 0.03 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 189 HIS 0.007 0.001 HIS A 239 PHE 0.030 0.002 PHE B 88 TYR 0.041 0.002 TYR H 90 ARG 0.017 0.001 ARG H 216 *********************** 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 211 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.295 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: A 68 MET cc_start: 0.8425 (tpp) cc_final: 0.8221 (mmm) REVERT: A 160 LEU cc_start: 0.8776 (pt) cc_final: 0.8176 (tp) REVERT: A 256 MET cc_start: 0.9412 (tpt) cc_final: 0.8616 (tpt) REVERT: A 317 TRP cc_start: 0.9094 (t60) cc_final: 0.8682 (t60) REVERT: A 318 LEU cc_start: 0.9758 (mt) cc_final: 0.9495 (pp) REVERT: A 349 GLU cc_start: 0.9252 (tt0) cc_final: 0.8832 (tt0) REVERT: A 458 GLU cc_start: 0.8920 (tt0) cc_final: 0.8379 (tt0) REVERT: A 494 MET cc_start: 0.8412 (ttm) cc_final: 0.8125 (ttm) REVERT: A 543 MET cc_start: 0.8325 (tpp) cc_final: 0.8015 (tpp) REVERT: A 649 PHE cc_start: 0.8368 (m-80) cc_final: 0.8121 (m-80) REVERT: A 668 MET cc_start: 0.8439 (mpp) cc_final: 0.8223 (mpp) REVERT: B 106 GLU cc_start: 0.9300 (tt0) cc_final: 0.8780 (pt0) REVERT: C 73 ASP cc_start: 0.8482 (t0) cc_final: 0.8111 (t0) REVERT: C 81 TRP cc_start: 0.8636 (m-90) cc_final: 0.7776 (m100) REVERT: C 92 GLN cc_start: 0.9273 (mm110) cc_final: 0.9029 (mm110) REVERT: C 105 ARG cc_start: 0.9375 (tpp80) cc_final: 0.9102 (tpp80) REVERT: C 116 PHE cc_start: 0.8158 (m-80) cc_final: 0.7240 (m-80) REVERT: C 117 TYR cc_start: 0.8891 (m-10) cc_final: 0.8488 (m-10) REVERT: C 171 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7177 (tm-30) REVERT: H 212 LYS cc_start: 0.9205 (tttm) cc_final: 0.8474 (mmtt) REVERT: H 215 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7484 (tptp) REVERT: L 3 GLU cc_start: 0.8847 (tt0) cc_final: 0.8309 (tm-30) REVERT: L 4 LEU cc_start: 0.8555 (mm) cc_final: 0.8200 (tp) REVERT: L 49 TYR cc_start: 0.8716 (m-10) cc_final: 0.8296 (m-10) REVERT: L 86 TYR cc_start: 0.8477 (m-80) cc_final: 0.7985 (m-10) REVERT: L 99 TYR cc_start: 0.8227 (m-80) cc_final: 0.6067 (m-80) REVERT: L 143 PHE cc_start: 0.8748 (p90) cc_final: 0.8302 (p90) REVERT: L 197 CYS cc_start: 0.6985 (t) cc_final: 0.6453 (p) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2022 time to fit residues: 63.2562 Evaluate side-chains 156 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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: 2.9990 chunk 59 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 112 optimal weight: 0.0060 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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** B 30 HIS H 203 ASN H 205 ASN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10909 Z= 0.172 Angle : 0.603 12.465 14856 Z= 0.303 Chirality : 0.043 0.192 1735 Planarity : 0.005 0.056 1862 Dihedral : 5.893 55.475 1745 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.44 (0.23), residues: 1336 helix: 0.71 (0.28), residues: 320 sheet: 0.55 (0.27), residues: 324 loop : 0.08 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 50 HIS 0.006 0.001 HIS A 426 PHE 0.029 0.002 PHE B 88 TYR 0.017 0.001 TYR A 182 ARG 0.009 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 215 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.317 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: A 68 MET cc_start: 0.8439 (tpp) cc_final: 0.8219 (mmm) REVERT: A 160 LEU cc_start: 0.8712 (pt) cc_final: 0.8146 (tp) REVERT: A 256 MET cc_start: 0.9400 (tpt) cc_final: 0.8623 (tpt) REVERT: A 283 LEU cc_start: 0.9048 (mt) cc_final: 0.8836 (mt) REVERT: A 317 TRP cc_start: 0.9046 (t60) cc_final: 0.8662 (t60) REVERT: A 318 LEU cc_start: 0.9728 (mt) cc_final: 0.9423 (pp) REVERT: A 349 GLU cc_start: 0.9251 (tt0) cc_final: 0.8817 (tt0) REVERT: A 458 GLU cc_start: 0.8938 (tt0) cc_final: 0.8422 (tt0) REVERT: A 543 MET cc_start: 0.8353 (tpp) cc_final: 0.8074 (tpp) REVERT: A 649 PHE cc_start: 0.8384 (m-80) cc_final: 0.8148 (m-80) REVERT: A 668 MET cc_start: 0.8465 (mpp) cc_final: 0.8207 (mpp) REVERT: B 89 PHE cc_start: 0.8981 (m-80) cc_final: 0.8458 (m-80) REVERT: B 106 GLU cc_start: 0.9301 (tt0) cc_final: 0.8811 (pt0) REVERT: C 65 LYS cc_start: 0.8368 (tttt) cc_final: 0.7569 (tmtt) REVERT: C 73 ASP cc_start: 0.8413 (t0) cc_final: 0.8078 (t0) REVERT: C 81 TRP cc_start: 0.8532 (m-90) cc_final: 0.7980 (m100) REVERT: C 92 GLN cc_start: 0.9271 (mm110) cc_final: 0.9019 (mm110) REVERT: C 105 ARG cc_start: 0.9353 (tpp80) cc_final: 0.9071 (tpp80) REVERT: C 116 PHE cc_start: 0.8139 (m-80) cc_final: 0.7226 (m-80) REVERT: C 117 TYR cc_start: 0.8924 (m-10) cc_final: 0.8512 (m-10) REVERT: C 171 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7177 (tm-30) REVERT: H 108 TYR cc_start: 0.8891 (m-80) cc_final: 0.8244 (m-80) REVERT: H 215 LYS cc_start: 0.7956 (ttmm) cc_final: 0.7739 (tptp) REVERT: L 3 GLU cc_start: 0.8827 (tt0) cc_final: 0.8326 (tm-30) REVERT: L 4 LEU cc_start: 0.8585 (mm) cc_final: 0.8198 (tp) REVERT: L 86 TYR cc_start: 0.8479 (m-80) cc_final: 0.8008 (m-10) REVERT: L 143 PHE cc_start: 0.8722 (p90) cc_final: 0.8309 (p90) REVERT: L 197 CYS cc_start: 0.6918 (t) cc_final: 0.6425 (p) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1940 time to fit residues: 61.6402 Evaluate side-chains 162 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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: 5.9990 chunk 97 optimal weight: 0.0040 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- 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** B 30 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.066918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.051685 restraints weight = 48214.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.053538 restraints weight = 27694.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.054787 restraints weight = 18553.831| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10909 Z= 0.212 Angle : 0.607 14.374 14856 Z= 0.307 Chirality : 0.042 0.190 1735 Planarity : 0.005 0.043 1862 Dihedral : 5.909 55.236 1745 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.38 (0.23), residues: 1336 helix: 0.74 (0.28), residues: 317 sheet: 0.51 (0.27), residues: 327 loop : 0.00 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 189 HIS 0.006 0.001 HIS A 426 PHE 0.030 0.002 PHE B 88 TYR 0.039 0.002 TYR H 90 ARG 0.011 0.001 ARG H 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2313.67 seconds wall clock time: 42 minutes 50.23 seconds (2570.23 seconds total)