Starting phenix.real_space_refine on Sun Mar 17 11:33:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cec_30342/03_2024/7cec_30342.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cec_30342/03_2024/7cec_30342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cec_30342/03_2024/7cec_30342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cec_30342/03_2024/7cec_30342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cec_30342/03_2024/7cec_30342.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cec_30342/03_2024/7cec_30342.pdb" } resolution = 3.9 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= 0.005 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 Mn 3 7.51 5 S 93 5.16 5 C 11061 2.51 5 N 2996 2.21 5 O 3404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ASP 587": "OD1" <-> "OD2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2720": "NH1" <-> "NH2" Residue "C GLU 2721": "OE1" <-> "OE2" Residue "C ARG 2780": "NH1" <-> "NH2" Residue "C ARG 2848": "NH1" <-> "NH2" Residue "C PHE 2915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2916": "OE1" <-> "OE2" Residue "C ARG 2953": "NH1" <-> "NH2" Residue "C GLU 2995": "OE1" <-> "OE2" Residue "C ARG 3036": "NH1" <-> "NH2" Residue "C ARG 3078": "NH1" <-> "NH2" Residue "C TYR 3100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3158": "OD1" <-> "OD2" Residue "C ARG 3180": "NH1" <-> "NH2" Residue "C GLU 3239": "OE1" <-> "OE2" Residue "D GLU 1744": "OE1" <-> "OE2" Residue "D GLU 1748": "OE1" <-> "OE2" Residue "D ARG 1752": "NH1" <-> "NH2" Residue "D GLU 1755": "OE1" <-> "OE2" Residue "D ASP 1756": "OD1" <-> "OD2" Residue "D GLU 1760": "OE1" <-> "OE2" Residue "D GLU 1765": "OE1" <-> "OE2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F ARG 147": "NH1" <-> "NH2" Residue "F ARG 154": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 58": "NH1" <-> "NH2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17561 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4308 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 521} Chain breaks: 6 Chain: "B" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3320 Classifications: {'peptide': 427} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 407} Chain breaks: 2 Chain: "C" Number of atoms: 4421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 574, 4412 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 33, 'TRANS': 540} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 574, 4412 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 33, 'TRANS': 540} Chain breaks: 2 bond proxies already assigned to first conformer: 4498 Chain: "D" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'TRANS': 46} Chain: "E" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 357 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "F" Number of atoms: 1360 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1354 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Conformer: "B" Number of residues, atoms: 171, 1354 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} bond proxies already assigned to first conformer: 1375 Chain: "G" Number of atoms: 1252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1252 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 150} Chain: "H" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "I" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1080 Classifications: {'peptide': 140} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 129} Chain breaks: 1 Chain: "J" 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: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' CA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Unusual residues: {' MN': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN C2767 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C2767 " occ=0.50 Time building chain proxies: 11.56, per 1000 atoms: 0.66 Number of scatterers: 17561 At special positions: 0 Unit cell: (145.803, 192.549, 149.142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 3 24.99 Ca 4 19.99 S 93 16.00 O 3404 8.00 N 2996 7.00 C 11061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 71 " distance=2.06 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 131 " distance=2.04 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 539 " distance=2.02 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 444 " distance=2.03 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 44 " distance=2.01 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 55 " distance=2.03 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 281 " distance=2.02 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.04 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 442 " distance=2.03 Simple disulfide: pdb=" SG CYS C2723 " - pdb=" SG CYS E1585 " distance=2.04 Simple disulfide: pdb=" SG CYS C2899 " - pdb=" SG CYS C2929 " distance=2.04 Simple disulfide: pdb=" SG CYS C3090 " - pdb=" SG CYS C3115 " distance=2.02 Simple disulfide: pdb=" SG CYS C3261 " - pdb=" SG CYS C3292 " distance=2.04 Simple disulfide: pdb=" SG CYS D1785 " - pdb=" SG CYS E1600 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 112 " - pdb=" SG CYS G 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 112 " - pdb=" SG CYS I 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 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 BETA1-4 " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1004 " - " ASN A 261 " " NAG A1005 " - " ASN A 347 " " NAG B1004 " - " ASN B 249 " " NAG B1005 " - " ASN B 343 " " NAG B1006 " - " ASN B 386 " " NAG C3402 " - " ASN C3257 " " NAG J 1 " - " ASN C3287 " Time building additional restraints: 7.38 Conformation dependent library (CDL) restraints added in 4.4 seconds 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 35 sheets defined 19.7% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 161 through 165 removed outlier: 4.469A pdb=" N SER A 164 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS A 165 " --> pdb=" O PHE A 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 165' Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.515A pdb=" N TRP A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.513A pdb=" N HIS A 262 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 14 through 20 removed outlier: 3.558A pdb=" N CYS B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 135 through 157 removed outlier: 3.921A pdb=" N SER B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.671A pdb=" N GLN B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 267 through 272 removed outlier: 4.300A pdb=" N GLY B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 removed outlier: 3.917A pdb=" N HIS B 292 " --> pdb=" O THR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.836A pdb=" N LYS B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 332 removed outlier: 3.712A pdb=" N GLU B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'C' and resid 2706 through 2732 removed outlier: 3.707A pdb=" N LEU C2710 " --> pdb=" O HIS C2706 " (cutoff:3.500A) Processing helix chain 'C' and resid 2754 through 2758 removed outlier: 3.712A pdb=" N ALA C2757 " --> pdb=" O ALA C2754 " (cutoff:3.500A) Processing helix chain 'C' and resid 2870 through 2874 removed outlier: 4.035A pdb=" N PHE C2874 " --> pdb=" O PRO C2871 " (cutoff:3.500A) Processing helix chain 'C' and resid 2937 through 2942 Processing helix chain 'C' and resid 3056 through 3060 Processing helix chain 'C' and resid 3074 through 3081 removed outlier: 3.595A pdb=" N ARG C3079 " --> pdb=" O PRO C3075 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU C3080 " --> pdb=" O SER C3076 " (cutoff:3.500A) Processing helix chain 'C' and resid 3117 through 3121 removed outlier: 3.619A pdb=" N VAL C3121 " --> pdb=" O ASP C3118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1741 through 1785 Processing helix chain 'E' and resid 1567 through 1596 removed outlier: 3.805A pdb=" N TYR E1575 " --> pdb=" O ALA E1571 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN E1588 " --> pdb=" O LYS E1584 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU E1590 " --> pdb=" O ILE E1586 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP E1591 " --> pdb=" O ARG E1587 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.815A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 4.000A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 122 removed outlier: 3.620A pdb=" N LEU F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 164 removed outlier: 3.742A pdb=" N ASP F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Proline residue: F 156 - end of helix removed outlier: 3.570A pdb=" N LYS F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.633A pdb=" N ASP G 82 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing helix chain 'G' and resid 111 through 116 Processing helix chain 'G' and resid 119 through 159 removed outlier: 4.081A pdb=" N LEU G 130 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Proline residue: G 132 - end of helix Proline residue: G 151 - end of helix Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 124 through 156 Proline residue: I 132 - end of helix Proline residue: I 151 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 5.169A pdb=" N SER A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A 417 " --> pdb=" O ASP A 426 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA A 428 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY A 415 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLY A 430 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 413 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 30 removed outlier: 3.879A pdb=" N SER A 24 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 39 " --> pdb=" O CYS A 63 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 62 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR A 72 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 173 removed outlier: 3.650A pdb=" N ILE A 180 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 removed outlier: 4.384A pdb=" N HIS A 282 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS A 270 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 297 through 300 removed outlier: 5.709A pdb=" N GLN A 316 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY A 325 " --> pdb=" O GLN A 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 371 through 376 removed outlier: 3.675A pdb=" N ILE A 386 " --> pdb=" O GLN A 400 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 400 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 446 through 447 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.670A pdb=" N VAL A 476 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 525 through 531 removed outlier: 3.591A pdb=" N ALA A 592 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 67 through 71 removed outlier: 6.200A pdb=" N GLN B 98 " --> pdb=" O LYS B 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 94 through 95 removed outlier: 4.015A pdb=" N ILE B 408 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 111 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 206 removed outlier: 6.239A pdb=" N VAL B 202 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N SER B 166 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER B 204 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE B 164 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR B 127 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 165 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 254 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B 336 " --> pdb=" O THR B 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 2737 through 2740 removed outlier: 7.195A pdb=" N LYS C2763 " --> pdb=" O ASP C2903 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU C2905 " --> pdb=" O ALA C2761 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA C2761 " --> pdb=" O LEU C2905 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 2816 through 2819 removed outlier: 3.777A pdb=" N MET C2795 " --> pdb=" O MET C2785 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU C2799 " --> pdb=" O PHE C2781 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N PHE C2781 " --> pdb=" O LEU C2799 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE C2876 " --> pdb=" O LEU C2747 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN C2746 " --> pdb=" O GLU C2916 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 2954 through 2955 Processing sheet with id=AC1, first strand: chain 'C' and resid 3046 through 3052 removed outlier: 6.418A pdb=" N VAL C3041 " --> pdb=" O VAL C3048 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER C3050 " --> pdb=" O VAL C3039 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C3039 " --> pdb=" O SER C3050 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG C3042 " --> pdb=" O GLN C3028 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 2978 through 2980 removed outlier: 6.446A pdb=" N LEU C2991 " --> pdb=" O LEU C2979 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 2978 through 2980 removed outlier: 6.446A pdb=" N LEU C2991 " --> pdb=" O LEU C2979 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 3095 through 3096 Processing sheet with id=AC5, first strand: chain 'C' and resid 3220 through 3223 removed outlier: 7.256A pdb=" N LEU C3215 " --> pdb=" O GLN C3222 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY C3152 " --> pdb=" O ASN C3264 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN C3264 " --> pdb=" O GLY C3152 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N HIS C3154 " --> pdb=" O ILE C3262 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ILE C3262 " --> pdb=" O HIS C3154 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE C3258 " --> pdb=" O GLY C3129 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 3134 through 3136 removed outlier: 5.083A pdb=" N ARG C3243 " --> pdb=" O ALA C3166 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA C3166 " --> pdb=" O ARG C3243 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU C3161 " --> pdb=" O LEU C3176 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU C3176 " --> pdb=" O LEU C3161 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.186A pdb=" N THR F 33 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET F 34 " --> pdb=" O THR F 50 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.730A pdb=" N HIS F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.978A pdb=" N MET G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.978A pdb=" N MET G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.517A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL H 34 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.553A pdb=" N ALA I 13 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLN I 37 " --> pdb=" O PRO I 46 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 19 through 24 663 hydrogen bonds defined for protein. 1731 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: 7.29 Time building geometry restraints manager: 8.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3694 1.32 - 1.45: 4737 1.45 - 1.58: 9341 1.58 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 17908 Sorted by residual: bond pdb=" C ASP B 138 " pdb=" O ASP B 138 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.17e-02 7.31e+03 1.26e+01 bond pdb=" CA ALA B 342 " pdb=" C ALA B 342 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.34e-02 5.57e+03 1.15e+01 bond pdb=" C SER B 227 " pdb=" O SER B 227 " ideal model delta sigma weight residual 1.244 1.211 0.033 1.00e-02 1.00e+04 1.08e+01 bond pdb=" CB PHE B 164 " pdb=" CG PHE B 164 " ideal model delta sigma weight residual 1.502 1.427 0.075 2.30e-02 1.89e+03 1.07e+01 bond pdb=" CA PRO A 425 " pdb=" C PRO A 425 " ideal model delta sigma weight residual 1.522 1.560 -0.039 1.19e-02 7.06e+03 1.06e+01 ... (remaining 17903 not shown) Histogram of bond angle deviations from ideal: 94.72 - 102.87: 135 102.87 - 111.02: 6687 111.02 - 119.17: 8024 119.17 - 127.31: 9209 127.31 - 135.46: 175 Bond angle restraints: 24230 Sorted by residual: angle pdb=" C TYR A 424 " pdb=" N PRO A 425 " pdb=" CA PRO A 425 " ideal model delta sigma weight residual 119.83 109.15 10.68 1.08e+00 8.57e-01 9.78e+01 angle pdb=" N PRO A 425 " pdb=" CA PRO A 425 " pdb=" C PRO A 425 " ideal model delta sigma weight residual 111.03 121.46 -10.43 1.54e+00 4.22e-01 4.59e+01 angle pdb=" C THR C2836 " pdb=" N LEU C2837 " pdb=" CA LEU C2837 " ideal model delta sigma weight residual 120.38 128.70 -8.32 1.37e+00 5.33e-01 3.69e+01 angle pdb=" N ASP B 137 " pdb=" CA ASP B 137 " pdb=" C ASP B 137 " ideal model delta sigma weight residual 111.07 105.06 6.01 1.07e+00 8.73e-01 3.15e+01 angle pdb=" CA ALA B 342 " pdb=" C ALA B 342 " pdb=" N ASN B 343 " ideal model delta sigma weight residual 116.84 126.29 -9.45 1.71e+00 3.42e-01 3.06e+01 ... (remaining 24225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 9664 18.07 - 36.13: 1093 36.13 - 54.20: 154 54.20 - 72.27: 47 72.27 - 90.34: 16 Dihedral angle restraints: 10974 sinusoidal: 4551 harmonic: 6423 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual -86.00 -176.34 90.34 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS B 28 " pdb=" SG CYS B 28 " pdb=" SG CYS B 55 " pdb=" CB CYS B 55 " ideal model delta sinusoidal sigma weight residual 93.00 179.97 -86.97 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS B 7 " pdb=" SG CYS B 7 " pdb=" SG CYS B 25 " pdb=" CB CYS B 25 " ideal model delta sinusoidal sigma weight residual 93.00 179.57 -86.57 1 1.00e+01 1.00e-02 9.03e+01 ... (remaining 10971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 2674 0.260 - 0.521: 14 0.521 - 0.781: 0 0.781 - 1.042: 0 1.042 - 1.302: 1 Chirality restraints: 2689 Sorted by residual: chirality pdb=" C1 NAG A1005 " pdb=" ND2 ASN A 347 " pdb=" C2 NAG A1005 " pdb=" O5 NAG A1005 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.24e+01 chirality pdb=" C2 NAG B1005 " pdb=" C1 NAG B1005 " pdb=" C3 NAG B1005 " pdb=" N2 NAG B1005 " both_signs ideal model delta sigma weight residual False -2.49 -2.08 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C3287 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 2686 not shown) Planarity restraints: 3147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D1762 " -0.024 2.00e-02 2.50e+03 4.81e-02 2.32e+01 pdb=" C ALA D1762 " 0.083 2.00e-02 2.50e+03 pdb=" O ALA D1762 " -0.031 2.00e-02 2.50e+03 pdb=" N ARG D1763 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 134 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.34e+01 pdb=" C MET G 134 " 0.063 2.00e-02 2.50e+03 pdb=" O MET G 134 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU G 135 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D1758 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ALA D1758 " 0.063 2.00e-02 2.50e+03 pdb=" O ALA D1758 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN D1759 " -0.021 2.00e-02 2.50e+03 ... (remaining 3144 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 350 2.55 - 3.14: 13920 3.14 - 3.73: 30065 3.73 - 4.31: 40684 4.31 - 4.90: 64919 Nonbonded interactions: 149938 Sorted by model distance: nonbonded pdb=" OE1 GLU B 169 " pdb="MN MN B1001 " model vdw 1.965 2.320 nonbonded pdb=" OD1 ASP B 226 " pdb="MN MN B1001 " model vdw 1.970 2.320 nonbonded pdb=" OE2 GLU B 229 " pdb="MN MN B1002 " model vdw 1.972 2.320 nonbonded pdb=" OD1 ASP A 301 " pdb=" OD1 ASP A 305 " model vdw 2.014 3.040 nonbonded pdb=" OD1 ASP A 363 " pdb=" OD1 ASP A 367 " model vdw 2.027 3.040 ... (remaining 149933 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=0.50 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: 1.620 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: 0.020 Extract box with map and model: 6.360 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 53.330 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.106 17908 Z= 0.696 Angle : 1.180 14.651 24230 Z= 0.650 Chirality : 0.071 1.302 2689 Planarity : 0.008 0.067 3140 Dihedral : 15.059 89.094 6798 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.69 % Favored : 91.26 % Rotamer: Outliers : 1.15 % Allowed : 10.52 % Favored : 88.33 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.25 % 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: -3.76 (0.15), residues: 2202 helix: -2.78 (0.20), residues: 353 sheet: -2.37 (0.18), residues: 661 loop : -2.46 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 545 HIS 0.012 0.003 HIS A 28 PHE 0.036 0.004 PHE H 79 TYR 0.027 0.003 TYR C3163 ARG 0.012 0.001 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 2.047 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: B 137 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7651 (p0) REVERT: B 175 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: B 290 MET cc_start: 0.8963 (mmm) cc_final: 0.8728 (mmp) REVERT: C 3125 MET cc_start: 0.8906 (mmt) cc_final: 0.8697 (mmm) REVERT: E 1587 ARG cc_start: 0.9130 (mtt180) cc_final: 0.8874 (ptp-110) REVERT: I 133 MET cc_start: 0.8380 (tpt) cc_final: 0.7356 (ptt) outliers start: 22 outliers final: 10 residues processed: 128 average time/residue: 0.3422 time to fit residues: 64.8724 Evaluate side-chains 78 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 2868 ASN Chi-restraints excluded: chain G residue 83 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 308 GLN A 388 HIS ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN A 485 ASN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 77 ASN B 109 GLN B 141 ASN B 292 HIS B 413 ASN C2706 HIS C2725 GLN C2805 HIS C2852 GLN C2959 GLN C2994 GLN C3015 GLN C3220 GLN ** D1750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1602 ASN F 39 GLN F 76 ASN F 105 GLN A ** F 105 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN H 76 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17908 Z= 0.197 Angle : 0.659 10.869 24230 Z= 0.339 Chirality : 0.047 0.657 2689 Planarity : 0.004 0.049 3140 Dihedral : 6.961 58.700 2624 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.77 % Allowed : 13.18 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.90 (0.16), residues: 2202 helix: -1.50 (0.24), residues: 359 sheet: -1.87 (0.19), residues: 611 loop : -2.10 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 36 HIS 0.003 0.001 HIS C3130 PHE 0.014 0.002 PHE A 253 TYR 0.016 0.001 TYR C3163 ARG 0.005 0.000 ARG E1593 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 86 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7886 (ptt) REVERT: B 137 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7661 (p0) REVERT: B 173 MET cc_start: 0.8933 (tpp) cc_final: 0.8690 (mmm) REVERT: C 2783 MET cc_start: 0.9161 (ppp) cc_final: 0.8918 (ppp) REVERT: C 2795 MET cc_start: 0.8637 (tmm) cc_final: 0.8131 (tmm) REVERT: C 2902 MET cc_start: 0.7921 (tpp) cc_final: 0.7597 (mmt) REVERT: E 1579 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9240 (mm) REVERT: F 139 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8301 (ttt) REVERT: H 0 MET cc_start: 0.8205 (ppp) cc_final: 0.7984 (ppp) REVERT: I 21 MET cc_start: 0.9056 (mpp) cc_final: 0.8267 (tmm) outliers start: 33 outliers final: 15 residues processed: 115 average time/residue: 0.2854 time to fit residues: 52.6926 Evaluate side-chains 82 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 3257 ASN Chi-restraints excluded: chain E residue 1579 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 161 optimal weight: 0.2980 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 534 GLN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS B 309 ASN C3128 HIS ** D1750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1602 ASN ** F 105 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN G 150 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17908 Z= 0.391 Angle : 0.752 10.309 24230 Z= 0.384 Chirality : 0.048 0.680 2689 Planarity : 0.005 0.053 3140 Dihedral : 6.910 59.253 2614 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.81 % Allowed : 16.15 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.68 (0.17), residues: 2202 helix: -0.79 (0.25), residues: 361 sheet: -1.87 (0.19), residues: 644 loop : -2.04 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C2939 HIS 0.005 0.002 HIS C2841 PHE 0.023 0.002 PHE A 354 TYR 0.016 0.002 TYR A 387 ARG 0.007 0.001 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 66 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 MET cc_start: 0.8060 (ptt) cc_final: 0.7842 (ptt) REVERT: B 137 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8044 (p0) REVERT: B 173 MET cc_start: 0.9051 (tpp) cc_final: 0.8738 (mmm) REVERT: C 2783 MET cc_start: 0.9186 (ppp) cc_final: 0.8983 (ppp) REVERT: C 2902 MET cc_start: 0.8130 (tpp) cc_final: 0.7706 (mmt) REVERT: C 3224 MET cc_start: 0.7336 (tpt) cc_final: 0.6850 (tpt) REVERT: F 139 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8295 (ttp) REVERT: I 21 MET cc_start: 0.8989 (mpp) cc_final: 0.8355 (tmm) REVERT: I 134 MET cc_start: 0.5537 (tpt) cc_final: 0.4812 (ptm) outliers start: 53 outliers final: 37 residues processed: 113 average time/residue: 0.2565 time to fit residues: 48.1239 Evaluate side-chains 98 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 59 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3154 HIS Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain E residue 1592 ILE Chi-restraints excluded: chain E residue 1595 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 133 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 30.0000 chunk 151 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 213 optimal weight: 50.0000 chunk 105 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** D1750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 17908 Z= 0.533 Angle : 0.853 9.628 24230 Z= 0.433 Chirality : 0.050 0.686 2689 Planarity : 0.005 0.042 3140 Dihedral : 7.212 59.989 2612 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 30.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 4.27 % Allowed : 17.92 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.87 (0.17), residues: 2202 helix: -0.51 (0.26), residues: 353 sheet: -2.12 (0.19), residues: 650 loop : -2.22 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C2939 HIS 0.008 0.002 HIS C2841 PHE 0.024 0.003 PHE A 354 TYR 0.019 0.002 TYR C3163 ARG 0.007 0.001 ARG G 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 58 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.4318 (mtt) cc_final: 0.3997 (mtt) REVERT: A 417 MET cc_start: 0.8251 (tpp) cc_final: 0.8043 (tpp) REVERT: A 540 MET cc_start: 0.7924 (ptt) cc_final: 0.7715 (ptt) REVERT: B 137 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8028 (p0) REVERT: B 172 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8695 (p) REVERT: B 173 MET cc_start: 0.9057 (tpp) cc_final: 0.8657 (mpp) REVERT: B 229 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: B 290 MET cc_start: 0.9141 (mmp) cc_final: 0.8901 (mmp) REVERT: C 2783 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8827 (ppp) REVERT: C 2795 MET cc_start: 0.8144 (tmm) cc_final: 0.7575 (tmm) REVERT: C 2902 MET cc_start: 0.8221 (tpp) cc_final: 0.7773 (mmt) REVERT: C 3224 MET cc_start: 0.7446 (tpt) cc_final: 0.6841 (tpt) REVERT: E 1573 MET cc_start: 0.9696 (tpp) cc_final: 0.9462 (tmm) REVERT: E 1574 ASP cc_start: 0.9213 (p0) cc_final: 0.8932 (p0) REVERT: E 1577 ARG cc_start: 0.9504 (mtm110) cc_final: 0.9201 (mtm110) REVERT: F 139 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8323 (ttp) outliers start: 81 outliers final: 51 residues processed: 132 average time/residue: 0.2498 time to fit residues: 55.9517 Evaluate side-chains 113 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 57 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 2783 MET Chi-restraints excluded: chain C residue 2984 GLN Chi-restraints excluded: chain C residue 3121 VAL Chi-restraints excluded: chain C residue 3127 PHE Chi-restraints excluded: chain C residue 3154 HIS Chi-restraints excluded: chain C residue 3257 ASN Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3271 LEU Chi-restraints excluded: chain E residue 1576 ASN Chi-restraints excluded: chain E residue 1592 ILE Chi-restraints excluded: chain E residue 1595 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 133 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 147 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1602 ASN ** F 105 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17908 Z= 0.174 Angle : 0.632 11.978 24230 Z= 0.319 Chirality : 0.046 0.561 2689 Planarity : 0.004 0.044 3140 Dihedral : 6.429 58.113 2612 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.34 % Allowed : 19.64 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.33 (0.17), residues: 2202 helix: 0.00 (0.27), residues: 362 sheet: -1.80 (0.19), residues: 629 loop : -1.89 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 103 HIS 0.005 0.001 HIS A 388 PHE 0.014 0.001 PHE B 115 TYR 0.028 0.001 TYR G 36 ARG 0.004 0.000 ARG F 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 72 time to evaluate : 2.081 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: A 144 MET cc_start: 0.4321 (mtt) cc_final: 0.3983 (mtt) REVERT: A 417 MET cc_start: 0.8300 (tpp) cc_final: 0.7977 (tpp) REVERT: A 540 MET cc_start: 0.8073 (ptt) cc_final: 0.7805 (ptt) REVERT: B 137 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7762 (p0) REVERT: B 290 MET cc_start: 0.9099 (mmp) cc_final: 0.8874 (mmp) REVERT: C 2783 MET cc_start: 0.9337 (ppp) cc_final: 0.9025 (ppp) REVERT: C 2785 MET cc_start: 0.8994 (ptm) cc_final: 0.8501 (ptm) REVERT: C 2820 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7363 (mm) REVERT: C 2902 MET cc_start: 0.7970 (tpp) cc_final: 0.7552 (mmt) REVERT: C 3125 MET cc_start: 0.8750 (mmt) cc_final: 0.8483 (mmt) REVERT: C 3224 MET cc_start: 0.6820 (tpt) cc_final: 0.6152 (tpt) REVERT: E 1573 MET cc_start: 0.9721 (tpp) cc_final: 0.9451 (tmm) REVERT: E 1574 ASP cc_start: 0.9111 (p0) cc_final: 0.8802 (p0) REVERT: E 1577 ARG cc_start: 0.9486 (mtm110) cc_final: 0.9197 (mtm110) REVERT: E 1578 ASP cc_start: 0.8843 (m-30) cc_final: 0.8625 (m-30) REVERT: F 139 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8184 (ttp) REVERT: I 21 MET cc_start: 0.8926 (mpp) cc_final: 0.8318 (tmm) outliers start: 44 outliers final: 27 residues processed: 112 average time/residue: 0.2627 time to fit residues: 48.6488 Evaluate side-chains 96 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 66 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 2984 GLN Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3154 HIS Chi-restraints excluded: chain C residue 3257 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 213 optimal weight: 50.0000 chunk 177 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 70 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN ** D1750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17908 Z= 0.186 Angle : 0.627 15.230 24230 Z= 0.312 Chirality : 0.046 0.560 2689 Planarity : 0.003 0.045 3140 Dihedral : 6.108 58.253 2610 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.03 % Allowed : 20.26 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.07 (0.17), residues: 2202 helix: 0.24 (0.27), residues: 362 sheet: -1.61 (0.19), residues: 626 loop : -1.75 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 190 HIS 0.003 0.001 HIS A 388 PHE 0.013 0.001 PHE B 115 TYR 0.019 0.001 TYR G 36 ARG 0.002 0.000 ARG I 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 69 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.4324 (mtt) cc_final: 0.3964 (mtt) REVERT: A 417 MET cc_start: 0.8302 (tpp) cc_final: 0.7987 (tpp) REVERT: A 540 MET cc_start: 0.8085 (ptt) cc_final: 0.7837 (ptt) REVERT: C 2783 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.9008 (ppp) REVERT: C 2820 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7456 (mm) REVERT: C 2902 MET cc_start: 0.8018 (tpp) cc_final: 0.7590 (mmt) REVERT: C 3125 MET cc_start: 0.8892 (mmt) cc_final: 0.8591 (mmt) REVERT: C 3224 MET cc_start: 0.6956 (tpt) cc_final: 0.6235 (tpt) REVERT: E 1573 MET cc_start: 0.9716 (tpp) cc_final: 0.9429 (tmm) REVERT: E 1574 ASP cc_start: 0.9102 (p0) cc_final: 0.8797 (p0) REVERT: E 1577 ARG cc_start: 0.9510 (mtm110) cc_final: 0.9205 (mtm110) REVERT: G 78 MET cc_start: 0.8316 (tpp) cc_final: 0.7398 (tpp) REVERT: I 21 MET cc_start: 0.8913 (mpp) cc_final: 0.8377 (tmm) outliers start: 38 outliers final: 33 residues processed: 101 average time/residue: 0.2742 time to fit residues: 45.9603 Evaluate side-chains 98 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 63 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 2783 MET Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 2842 MET Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3127 PHE Chi-restraints excluded: chain C residue 3257 ASN Chi-restraints excluded: chain C residue 3271 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 133 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 213 optimal weight: 50.0000 chunk 133 optimal weight: 0.1980 chunk 129 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17908 Z= 0.280 Angle : 0.666 12.646 24230 Z= 0.331 Chirality : 0.046 0.580 2689 Planarity : 0.004 0.043 3140 Dihedral : 6.131 58.592 2608 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.97 % Allowed : 20.05 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.14 (0.17), residues: 2202 helix: 0.41 (0.27), residues: 362 sheet: -1.74 (0.19), residues: 638 loop : -1.81 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 190 HIS 0.004 0.001 HIS B 292 PHE 0.019 0.002 PHE A 354 TYR 0.021 0.001 TYR G 36 ARG 0.003 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 63 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.4454 (mtt) cc_final: 0.4062 (mtt) REVERT: A 417 MET cc_start: 0.8262 (tpp) cc_final: 0.7943 (tpp) REVERT: A 540 MET cc_start: 0.8047 (ptt) cc_final: 0.7798 (ptt) REVERT: B 229 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8076 (mm-30) REVERT: B 310 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8693 (t0) REVERT: C 2783 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9021 (ppp) REVERT: C 2795 MET cc_start: 0.8507 (tmm) cc_final: 0.8197 (tmm) REVERT: C 2820 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7497 (mm) REVERT: C 2902 MET cc_start: 0.8141 (tpp) cc_final: 0.7648 (mmt) REVERT: C 3125 MET cc_start: 0.8885 (mmt) cc_final: 0.8585 (mmt) REVERT: C 3224 MET cc_start: 0.7119 (tpt) cc_final: 0.6291 (tpt) REVERT: E 1573 MET cc_start: 0.9720 (tpp) cc_final: 0.9486 (tmm) REVERT: E 1574 ASP cc_start: 0.9134 (p0) cc_final: 0.8776 (p0) REVERT: E 1577 ARG cc_start: 0.9530 (mtm110) cc_final: 0.9246 (mtm110) REVERT: I 21 MET cc_start: 0.8924 (mpp) cc_final: 0.8399 (tmm) outliers start: 56 outliers final: 40 residues processed: 112 average time/residue: 0.2755 time to fit residues: 50.3627 Evaluate side-chains 105 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 61 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 2783 MET Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 2984 GLN Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3154 HIS Chi-restraints excluded: chain C residue 3257 ASN Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3271 LEU Chi-restraints excluded: chain E residue 1592 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 133 MET Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 135 optimal weight: 0.2980 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17908 Z= 0.288 Angle : 0.670 12.478 24230 Z= 0.333 Chirality : 0.046 0.568 2689 Planarity : 0.004 0.045 3140 Dihedral : 6.175 58.660 2608 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.02 % Allowed : 20.52 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.14 (0.17), residues: 2202 helix: 0.50 (0.27), residues: 362 sheet: -1.78 (0.19), residues: 638 loop : -1.82 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 190 HIS 0.004 0.001 HIS C2841 PHE 0.019 0.002 PHE A 354 TYR 0.015 0.001 TYR C3163 ARG 0.003 0.000 ARG G 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 62 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.4537 (mtt) cc_final: 0.4069 (mtt) REVERT: A 417 MET cc_start: 0.8290 (tpp) cc_final: 0.7963 (tpp) REVERT: A 540 MET cc_start: 0.8046 (ptt) cc_final: 0.7796 (ptt) REVERT: B 229 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8095 (mm-30) REVERT: B 310 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8682 (t0) REVERT: C 2783 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.9112 (ppp) REVERT: C 2820 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7462 (mm) REVERT: C 2902 MET cc_start: 0.8148 (tpp) cc_final: 0.7647 (mmt) REVERT: C 3125 MET cc_start: 0.8897 (mmt) cc_final: 0.8570 (mmt) REVERT: C 3224 MET cc_start: 0.7102 (tpt) cc_final: 0.6375 (tpt) REVERT: E 1573 MET cc_start: 0.9734 (tpp) cc_final: 0.9515 (tmm) REVERT: E 1574 ASP cc_start: 0.9126 (p0) cc_final: 0.8782 (p0) REVERT: E 1577 ARG cc_start: 0.9549 (mtm110) cc_final: 0.9261 (mtm110) REVERT: I 21 MET cc_start: 0.8930 (mpp) cc_final: 0.8427 (tmm) outliers start: 57 outliers final: 49 residues processed: 114 average time/residue: 0.2725 time to fit residues: 51.3852 Evaluate side-chains 113 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 60 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 2783 MET Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 2984 GLN Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3121 VAL Chi-restraints excluded: chain C residue 3154 HIS Chi-restraints excluded: chain C residue 3257 ASN Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3271 LEU Chi-restraints excluded: chain E residue 1592 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 133 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 198 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 197 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17908 Z= 0.364 Angle : 0.731 12.615 24230 Z= 0.363 Chirality : 0.047 0.601 2689 Planarity : 0.004 0.047 3140 Dihedral : 6.375 58.687 2608 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 3.07 % Allowed : 20.83 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.27 (0.17), residues: 2202 helix: 0.46 (0.27), residues: 362 sheet: -1.88 (0.19), residues: 633 loop : -1.93 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C2939 HIS 0.005 0.001 HIS C2841 PHE 0.021 0.002 PHE A 354 TYR 0.017 0.002 TYR C3163 ARG 0.004 0.001 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 61 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.4645 (mtt) cc_final: 0.4139 (mtt) REVERT: A 417 MET cc_start: 0.8309 (tpp) cc_final: 0.7951 (tpp) REVERT: A 540 MET cc_start: 0.8012 (ptt) cc_final: 0.7788 (ptt) REVERT: B 229 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8149 (mm-30) REVERT: B 310 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8638 (t0) REVERT: C 2783 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.9064 (ppp) REVERT: C 2820 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7487 (mm) REVERT: C 2902 MET cc_start: 0.8167 (tpp) cc_final: 0.7659 (mmt) REVERT: C 3125 MET cc_start: 0.8927 (mmt) cc_final: 0.8539 (mmt) REVERT: C 3224 MET cc_start: 0.7349 (tpt) cc_final: 0.6946 (tpt) REVERT: G 78 MET cc_start: 0.8127 (tpt) cc_final: 0.7815 (tpp) REVERT: I 21 MET cc_start: 0.8986 (mpp) cc_final: 0.8487 (tmm) outliers start: 58 outliers final: 52 residues processed: 114 average time/residue: 0.2535 time to fit residues: 48.5835 Evaluate side-chains 116 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 60 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 2783 MET Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 2963 THR Chi-restraints excluded: chain C residue 2984 GLN Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3121 VAL Chi-restraints excluded: chain C residue 3127 PHE Chi-restraints excluded: chain C residue 3154 HIS Chi-restraints excluded: chain C residue 3257 ASN Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3271 LEU Chi-restraints excluded: chain E residue 1592 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 133 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 145 optimal weight: 0.5980 chunk 220 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 139 optimal weight: 0.0970 overall best weight: 2.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17908 Z= 0.246 Angle : 0.672 13.314 24230 Z= 0.332 Chirality : 0.046 0.568 2689 Planarity : 0.004 0.047 3140 Dihedral : 6.145 59.300 2608 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.97 % Allowed : 21.15 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.08 (0.17), residues: 2202 helix: 0.71 (0.27), residues: 362 sheet: -1.81 (0.19), residues: 642 loop : -1.80 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 190 HIS 0.003 0.001 HIS B 292 PHE 0.016 0.002 PHE A 354 TYR 0.016 0.001 TYR G 36 ARG 0.009 0.000 ARG E1577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 64 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.4640 (mtt) cc_final: 0.4162 (mtt) REVERT: A 417 MET cc_start: 0.8337 (tpp) cc_final: 0.7988 (tpp) REVERT: A 540 MET cc_start: 0.8013 (ptt) cc_final: 0.7770 (ptt) REVERT: B 229 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8230 (mm-30) REVERT: B 310 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8641 (t0) REVERT: C 2783 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.9109 (ppp) REVERT: C 2795 MET cc_start: 0.8460 (tmm) cc_final: 0.8115 (tmm) REVERT: C 2820 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7442 (mm) REVERT: C 3125 MET cc_start: 0.8924 (mmt) cc_final: 0.8533 (mmt) REVERT: C 3224 MET cc_start: 0.7140 (tpt) cc_final: 0.6511 (tpt) REVERT: G 78 MET cc_start: 0.8081 (tpt) cc_final: 0.7032 (tpp) REVERT: I 21 MET cc_start: 0.8922 (mpp) cc_final: 0.8474 (tmm) outliers start: 56 outliers final: 50 residues processed: 114 average time/residue: 0.2699 time to fit residues: 50.7191 Evaluate side-chains 116 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 62 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 2783 MET Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 2963 THR Chi-restraints excluded: chain C residue 2984 GLN Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3121 VAL Chi-restraints excluded: chain C residue 3127 PHE Chi-restraints excluded: chain C residue 3154 HIS Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3271 LEU Chi-restraints excluded: chain E residue 1592 ILE Chi-restraints excluded: chain E residue 1595 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 133 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 22 optimal weight: 0.0000 chunk 32 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1777 GLN ** F 105 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.039099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.028712 restraints weight = 351668.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.030109 restraints weight = 139079.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.031039 restraints weight = 77284.359| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17908 Z= 0.168 Angle : 0.641 13.789 24230 Z= 0.312 Chirality : 0.045 0.524 2689 Planarity : 0.003 0.048 3140 Dihedral : 5.735 57.704 2608 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.45 % Allowed : 21.61 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.17), residues: 2202 helix: 0.91 (0.28), residues: 360 sheet: -1.54 (0.20), residues: 635 loop : -1.67 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 190 HIS 0.003 0.001 HIS C2706 PHE 0.012 0.001 PHE B 115 TYR 0.015 0.001 TYR C3063 ARG 0.008 0.000 ARG E1577 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3186.82 seconds wall clock time: 59 minutes 15.71 seconds (3555.71 seconds total)