Starting phenix.real_space_refine (version: dev) on Sun Feb 19 20:51:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/02_2023/6c5v_7344_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/02_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_7344/02_2023/6c5v_7344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/02_2023/6c5v_7344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/02_2023/6c5v_7344_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c5v_7344/02_2023/6c5v_7344_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 4 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 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 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 chiralities: 3 Time building chain proxies: 5.88, 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: 4.38 Conformation dependent library (CDL) restraints added in 1.5 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: 1.31 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: 3.08 Time building geometry restraints manager: 4.73 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=" C2 NAG C 303 " pdb=" N2 NAG C 303 " ideal model delta sigma weight residual 1.454 1.504 -0.050 1.00e-02 1.00e+04 2.51e+01 bond pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " ideal model delta sigma weight residual 1.526 1.455 0.071 1.50e-02 4.44e+03 2.26e+01 bond pdb=" C7 NAG B 202 " pdb=" N2 NAG B 202 " ideal model delta sigma weight residual 1.337 1.285 0.052 1.10e-02 8.26e+03 2.25e+01 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=" C3 NAG B 202 " pdb=" C4 NAG B 202 " ideal model delta sigma weight residual 1.523 1.559 -0.036 1.00e-02 1.00e+04 1.29e+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=" C2 NAG C 303 " pdb=" C1 NAG C 303 " pdb=" O5 NAG C 303 " ideal model delta sigma weight residual 109.64 103.18 6.46 5.38e-01 3.45e+00 1.44e+02 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=" C2 NAG C 303 " pdb=" C3 NAG C 303 " pdb=" C4 NAG C 303 " ideal model delta sigma weight residual 110.39 99.48 10.91 1.16e+00 7.50e-01 8.92e+01 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 ... (remaining 14851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 6205 15.63 - 31.26: 183 31.26 - 46.89: 56 46.89 - 62.51: 31 62.51 - 78.14: 9 Dihedral angle restraints: 6484 sinusoidal: 2565 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 6481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1549 0.116 - 0.232: 173 0.232 - 0.349: 11 0.349 - 0.465: 1 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 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. 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.400 Check model and map are aligned: 0.170 Process input model: 30.020 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.100 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 0.082 10909 Z= 0.874 Angle : 1.296 22.578 14856 Z= 0.892 Chirality : 0.073 0.581 1735 Planarity : 0.006 0.040 1862 Dihedral : 9.982 78.144 3928 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 % 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 *********************** 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 : 1.298 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: 0.2352 time to fit residues: 129.6929 Evaluate side-chains 212 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.199 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1012 time to fit residues: 1.9174 ------------------------------------------------------------------------------- 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: 0.7942 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 10909 Z= 0.237 Angle : 0.660 7.921 14856 Z= 0.350 Chirality : 0.045 0.342 1735 Planarity : 0.005 0.042 1862 Dihedral : 4.743 29.822 1559 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 0.09 % 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: 0.68 (0.23), residues: 1336 helix: 0.65 (0.27), residues: 335 sheet: 0.84 (0.27), residues: 334 loop : 0.28 (0.25), residues: 667 *********************** 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 282 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 281 time to evaluate : 1.192 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: 282 average time/residue: 0.2200 time to fit residues: 88.6482 Evaluate side-chains 189 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7123 ------------------------------------------------------------------------------- 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: 10.0000 chunk 37 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.8041 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10909 Z= 0.245 Angle : 0.618 7.878 14856 Z= 0.326 Chirality : 0.043 0.217 1735 Planarity : 0.005 0.046 1862 Dihedral : 4.775 26.894 1559 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.17 % 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: 0.66 (0.23), residues: 1336 helix: 0.83 (0.27), residues: 329 sheet: 0.74 (0.27), residues: 326 loop : 0.22 (0.25), residues: 681 *********************** 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 250 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 248 time to evaluate : 1.140 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 outliers start: 2 outliers final: 2 residues processed: 250 average time/residue: 0.1984 time to fit residues: 73.5069 Evaluate side-chains 180 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 1.196 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0989 time to fit residues: 2.0603 ------------------------------------------------------------------------------- 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: 0.1980 chunk 90 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS H 31 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 10909 Z= 0.382 Angle : 0.729 8.750 14856 Z= 0.384 Chirality : 0.045 0.215 1735 Planarity : 0.005 0.045 1862 Dihedral : 5.316 26.383 1559 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.00 % 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: 0.10 (0.23), residues: 1336 helix: 0.13 (0.26), residues: 324 sheet: 0.62 (0.28), residues: 315 loop : -0.12 (0.24), residues: 697 *********************** 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 218 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 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 outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2114 time to fit residues: 67.7396 Evaluate side-chains 159 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6484 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 0.0870 chunk 115 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 10909 Z= 0.283 Angle : 0.634 6.969 14856 Z= 0.337 Chirality : 0.043 0.197 1735 Planarity : 0.005 0.044 1862 Dihedral : 5.231 30.862 1559 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.00 % 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: 0.12 (0.23), residues: 1336 helix: 0.25 (0.27), residues: 327 sheet: 0.47 (0.27), residues: 320 loop : -0.08 (0.25), residues: 689 *********************** 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 218 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.541 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: 218 average time/residue: 0.2032 time to fit residues: 65.8340 Evaluate side-chains 154 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6282 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS A 598 GLN C 103 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 10909 Z= 0.309 Angle : 0.664 9.805 14856 Z= 0.347 Chirality : 0.044 0.214 1735 Planarity : 0.005 0.044 1862 Dihedral : 5.343 31.778 1559 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.00 % 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 (0.23), residues: 1336 helix: 0.26 (0.27), residues: 324 sheet: 0.46 (0.27), residues: 313 loop : -0.15 (0.25), residues: 699 *********************** 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 208 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.311 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 outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2083 time to fit residues: 64.9655 Evaluate side-chains 151 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6869 ------------------------------------------------------------------------------- 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: 8.9990 chunk 14 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 10909 Z= 0.349 Angle : 0.704 8.196 14856 Z= 0.370 Chirality : 0.044 0.230 1735 Planarity : 0.005 0.047 1862 Dihedral : 5.500 27.971 1559 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.00 % 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: 0.06 (0.27), residues: 322 sheet: 0.23 (0.27), residues: 311 loop : -0.33 (0.25), residues: 703 *********************** 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 201 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.321 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: 201 average time/residue: 0.2242 time to fit residues: 67.2532 Evaluate side-chains 147 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7701 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5816 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= 0.187 Angle : 0.600 6.504 14856 Z= 0.312 Chirality : 0.043 0.218 1735 Planarity : 0.005 0.044 1862 Dihedral : 5.069 27.734 1559 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.00 % 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: 0.63 (0.27), residues: 316 sheet: 0.50 (0.27), residues: 308 loop : -0.18 (0.25), residues: 712 *********************** 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 207 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.575 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: 207 average time/residue: 0.2232 time to fit residues: 67.2617 Evaluate side-chains 146 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8427 ------------------------------------------------------------------------------- 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: 3.9990 chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 0.0050 chunk 119 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- 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** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN H 205 ASN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 10909 Z= 0.235 Angle : 0.620 8.572 14856 Z= 0.320 Chirality : 0.043 0.194 1735 Planarity : 0.005 0.045 1862 Dihedral : 5.076 29.057 1559 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.00 % 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: 0.11 (0.23), residues: 1336 helix: 0.53 (0.27), residues: 319 sheet: 0.36 (0.27), residues: 318 loop : -0.18 (0.25), residues: 699 *********************** 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 196 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.363 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: 196 average time/residue: 0.2093 time to fit residues: 60.1929 Evaluate side-chains 148 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6371 ------------------------------------------------------------------------------- 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: 0.0770 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 0.0870 chunk 83 optimal weight: 6.9990 chunk 112 optimal weight: 0.1980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.6059 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= 0.175 Angle : 0.611 10.616 14856 Z= 0.311 Chirality : 0.043 0.353 1735 Planarity : 0.005 0.045 1862 Dihedral : 4.908 27.490 1559 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.00 % 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: 0.53 (0.27), residues: 316 sheet: 0.43 (0.28), residues: 313 loop : -0.04 (0.25), residues: 707 ********************** 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 189 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.187 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: 189 average time/residue: 0.2081 time to fit residues: 58.2432 Evaluate side-chains 148 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7520 ------------------------------------------------------------------------------- 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: 4.9990 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 0.0020 chunk 108 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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** ** 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 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.052594 restraints weight = 48540.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.054439 restraints weight = 28094.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.055685 restraints weight = 18854.037| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.6214 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= 0.208 Angle : 0.619 8.453 14856 Z= 0.316 Chirality : 0.043 0.288 1735 Planarity : 0.005 0.045 1862 Dihedral : 4.917 27.465 1559 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.00 % 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: 0.57 (0.28), residues: 309 sheet: 0.42 (0.28), residues: 319 loop : -0.06 (0.25), residues: 708 =============================================================================== Job complete usr+sys time: 2209.07 seconds wall clock time: 41 minutes 38.83 seconds (2498.83 seconds total)