Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 20 07:10:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr4_27670/10_2023/8dr4_27670_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr4_27670/10_2023/8dr4_27670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr4_27670/10_2023/8dr4_27670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr4_27670/10_2023/8dr4_27670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr4_27670/10_2023/8dr4_27670_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr4_27670/10_2023/8dr4_27670_trim.pdb" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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: 7 Type Number sf(0) Gaussians P 76 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 13640 2.51 5 N 3747 2.21 5 O 4354 1.98 5 H 21549 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 504": "OD1" <-> "OD2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 715": "OD1" <-> "OD2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "A ASP 734": "OD1" <-> "OD2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "A ASP 743": "OD1" <-> "OD2" Residue "A GLU 747": "OE1" <-> "OE2" Residue "A ASP 753": "OD1" <-> "OD2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C ASP 243": "OD1" <-> "OD2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D ASP 312": "OD1" <-> "OD2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "F ASP 93": "OD1" <-> "OD2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F GLU 143": "OE1" <-> "OE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F ASP 172": "OD1" <-> "OD2" Residue "F ASP 223": "OD1" <-> "OD2" Residue "F PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H ASP 134": "OD1" <-> "OD2" Residue "H ASP 172": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 43471 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7919 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 19, 'TRANS': 477} Chain: "B" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5084 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 5253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5253 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 5282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5282 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 319} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 5675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5675 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "F" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4044 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 4037 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 4060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4060 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 616 Classifications: {'DNA': 19} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 18} Chain: "J" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 553 Classifications: {'DNA': 18} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 17} Chain: "K" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 395 Classifications: {'DNA': 12} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 11} Chain: "L" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 397 Classifications: {'DNA': 13} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.14, per 1000 atoms: 0.44 Number of scatterers: 43471 At special positions: 0 Unit cell: (132.986, 120.596, 143.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 76 15.00 Mg 4 11.99 O 4354 8.00 N 3747 7.00 C 13640 6.00 H 21549 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.18 Conformation dependent library (CDL) restraints added in 3.3 seconds 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 17 sheets defined 54.8% alpha, 14.8% beta 20 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 18.91 Creating SS restraints... Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 342 through 346 removed outlier: 4.127A pdb=" N VAL A 345 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 346 " --> pdb=" O SER A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 391 through 396 removed outlier: 4.009A pdb=" N ALA A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 414 through 417 removed outlier: 4.175A pdb=" N LYS A 417 " --> pdb=" O LEU A 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 417' Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 460 through 467 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 479 through 482 Processing helix chain 'A' and resid 483 through 495 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.753A pdb=" N THR A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 544 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 561 through 564 Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 573 through 583 Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 649 through 656 Processing helix chain 'A' and resid 668 through 690 Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 704 through 712 removed outlier: 4.271A pdb=" N THR A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 720 removed outlier: 3.623A pdb=" N LEU A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 723 No H-bonds generated for 'chain 'A' and resid 721 through 723' Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 738 through 747 Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.806A pdb=" N VAL A 754 " --> pdb=" O GLY A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 763 through 776 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.729A pdb=" N ILE B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.824A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.659A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 215 removed outlier: 4.298A pdb=" N VAL B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.637A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.538A pdb=" N GLY B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.539A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.569A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 4.204A pdb=" N SER C 76 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 102 removed outlier: 3.945A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.562A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.580A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.758A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 3.987A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.911A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.875A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.667A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 91 Proline residue: D 85 - end of helix removed outlier: 4.875A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.899A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.447A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.782A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 Processing helix chain 'D' and resid 315 through 334 removed outlier: 3.601A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.305A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 97 through 103 removed outlier: 7.014A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.751A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYS E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.527A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR E 161 " --> pdb=" O THR E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 226 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.760A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 353 removed outlier: 3.843A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 18 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 81 removed outlier: 3.640A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.568A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 removed outlier: 3.806A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.883A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.770A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 removed outlier: 4.463A pdb=" N SER G 220 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 18 removed outlier: 4.218A pdb=" N PHE H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 81 removed outlier: 3.816A pdb=" N CYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 153 removed outlier: 3.735A pdb=" N GLN H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 209 through 218 removed outlier: 3.570A pdb=" N GLY H 218 " --> pdb=" O ASP H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 377 removed outlier: 6.299A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA A 348 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE A 473 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N MET A 350 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.990A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 601 removed outlier: 3.531A pdb=" N HIS A 659 " --> pdb=" O ARG A 600 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.325A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.412A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.775A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.585A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 76 removed outlier: 6.527A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.334A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.890A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG F 110 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL H 203 " --> pdb=" O ILE H 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.206A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY F 34 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 203 through 208 removed outlier: 5.849A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE G 111 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU G 59 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.567A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 177 through 182 removed outlier: 4.109A pdb=" N GLY G 178 " --> pdb=" O ALA G 171 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB7, first strand: chain 'H' and resid 66 through 68 removed outlier: 3.592A pdb=" N LEU H 250 " --> pdb=" O ALA H 235 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA H 235 " --> pdb=" O LEU H 250 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 89 through 91 1139 hydrogen bonds defined for protein. 3183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 18.13 Time building geometry restraints manager: 39.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 21510 1.05 - 1.27: 3620 1.27 - 1.49: 8892 1.49 - 1.70: 9774 1.70 - 1.92: 159 Bond restraints: 43955 Sorted by residual: bond pdb=" C2' AGS D 402 " pdb=" C3' AGS D 402 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.00e+02 bond pdb=" C2' AGS A1001 " pdb=" C3' AGS A1001 " ideal model delta sigma weight residual 1.530 1.240 0.290 1.30e-02 5.92e+03 4.97e+02 bond pdb=" C2' AGS C 402 " pdb=" C3' AGS C 402 " ideal model delta sigma weight residual 1.530 1.240 0.290 1.30e-02 5.92e+03 4.97e+02 bond pdb=" C2' AGS B 402 " pdb=" C3' AGS B 402 " ideal model delta sigma weight residual 1.530 1.241 0.289 1.30e-02 5.92e+03 4.95e+02 bond pdb=" C6 AGS C 402 " pdb=" N6 AGS C 402 " ideal model delta sigma weight residual 1.335 1.469 -0.134 1.00e-02 1.00e+04 1.79e+02 ... (remaining 43950 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.83: 907 106.83 - 113.62: 53412 113.62 - 120.41: 13872 120.41 - 127.20: 11273 127.20 - 133.99: 270 Bond angle restraints: 79734 Sorted by residual: angle pdb=" N1 AGS A1001 " pdb=" C2 AGS A1001 " pdb=" N3 AGS A1001 " ideal model delta sigma weight residual 128.80 120.08 8.72 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS D 402 " pdb=" C2 AGS D 402 " pdb=" N3 AGS D 402 " ideal model delta sigma weight residual 128.80 120.11 8.69 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS C 402 " pdb=" C2 AGS C 402 " pdb=" N3 AGS C 402 " ideal model delta sigma weight residual 128.80 120.12 8.68 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS B 402 " pdb=" C2 AGS B 402 " pdb=" N3 AGS B 402 " ideal model delta sigma weight residual 128.80 120.13 8.67 8.41e-01 1.41e+00 1.06e+02 angle pdb=" C5 AGS C 402 " pdb=" N7 AGS C 402 " pdb=" C8 AGS C 402 " ideal model delta sigma weight residual 103.67 107.99 -4.32 4.26e-01 5.51e+00 1.03e+02 ... (remaining 79729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.08: 16552 32.08 - 64.16: 758 64.16 - 96.24: 48 96.24 - 128.32: 1 128.32 - 160.40: 4 Dihedral angle restraints: 17363 sinusoidal: 8747 harmonic: 8616 Sorted by residual: dihedral pdb=" O2B GDP E 401 " pdb=" O3A GDP E 401 " pdb=" PB GDP E 401 " pdb=" PA GDP E 401 " ideal model delta sinusoidal sigma weight residual 180.00 19.60 160.40 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' GDP E 401 " pdb=" O5' GDP E 401 " pdb=" PA GDP E 401 " pdb=" O3A GDP E 401 " ideal model delta sinusoidal sigma weight residual 179.98 -70.22 -109.80 1 2.00e+01 2.50e-03 3.21e+01 dihedral pdb=" O1A AGS D 402 " pdb=" O3A AGS D 402 " pdb=" PA AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sinusoidal sigma weight residual -67.73 73.26 -140.99 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 17360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3143 0.062 - 0.124: 386 0.124 - 0.187: 17 0.187 - 0.249: 4 0.249 - 0.311: 4 Chirality restraints: 3554 Sorted by residual: chirality pdb=" C2' AGS C 402 " pdb=" C1' AGS C 402 " pdb=" C3' AGS C 402 " pdb=" O2' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.36 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C2' AGS B 402 " pdb=" C1' AGS B 402 " pdb=" C3' AGS B 402 " pdb=" O2' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.36 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C2' AGS A1001 " pdb=" C1' AGS A1001 " pdb=" C3' AGS A1001 " pdb=" O2' AGS A1001 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 3551 not shown) Planarity restraints: 6223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO E 63 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 163 " 0.142 9.50e-02 1.11e+02 4.78e-02 2.96e+00 pdb=" NE ARG C 163 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 163 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 163 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 163 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG C 163 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG C 163 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG C 163 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG C 163 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 190 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO C 191 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 191 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 191 " -0.024 5.00e-02 4.00e+02 ... (remaining 6220 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 581 2.08 - 2.71: 71004 2.71 - 3.34: 127699 3.34 - 3.97: 166702 3.97 - 4.60: 257727 Nonbonded interactions: 623713 Sorted by model distance: nonbonded pdb=" OE1 GLU G 32 " pdb=" H GLU G 32 " model vdw 1.449 1.850 nonbonded pdb=" OE1 GLU A 740 " pdb=" H GLU A 740 " model vdw 1.494 1.850 nonbonded pdb=" OD2 ASP H 134 " pdb=" H SER H 231 " model vdw 1.578 1.850 nonbonded pdb=" O ALA C 326 " pdb=" HG SER C 330 " model vdw 1.600 1.850 nonbonded pdb=" OD1 ASN B 220 " pdb=" H ASN B 223 " model vdw 1.634 1.850 ... (remaining 623708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'F' and resid 1 through 255) selection = (chain 'G' and resid 1 through 255) selection = (chain 'H' and resid 1 through 255) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.590 Extract box with map and model: 14.360 Check model and map are aligned: 0.570 Set scattering table: 0.340 Process input model: 150.160 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.008 0.291 22406 Z= 0.379 Angle : 0.558 8.783 30563 Z= 0.384 Chirality : 0.040 0.311 3554 Planarity : 0.003 0.063 3666 Dihedral : 18.353 160.402 8545 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.91 % Allowed : 19.59 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.17), residues: 2584 helix: 2.08 (0.16), residues: 1225 sheet: 0.54 (0.22), residues: 523 loop : 0.52 (0.24), residues: 836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 332 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 311 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 330 average time/residue: 3.5129 time to fit residues: 1304.5369 Evaluate side-chains 208 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 3.366 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.7957 time to fit residues: 5.3645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 10.0000 chunk 197 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 203 optimal weight: 0.0020 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 236 optimal weight: 10.0000 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 546 ASN B 148 ASN B 188 ASN B 216 HIS B 320 ASN C 31 ASN C 184 HIS C 292 ASN D 24 GLN E 14 ASN E 32 GLN E 224 GLN E 336 ASN F 24 GLN G 38 GLN G 201 GLN ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22406 Z= 0.172 Angle : 0.502 6.785 30563 Z= 0.270 Chirality : 0.039 0.144 3554 Planarity : 0.003 0.040 3666 Dihedral : 14.681 169.202 3437 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.34 % Allowed : 19.90 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.17), residues: 2584 helix: 2.06 (0.15), residues: 1238 sheet: 0.47 (0.22), residues: 528 loop : 0.36 (0.23), residues: 818 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 247 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 193 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 19 residues processed: 239 average time/residue: 3.0270 time to fit residues: 827.4754 Evaluate side-chains 196 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 3.643 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 1.1552 time to fit residues: 7.3464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 255 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 80 optimal weight: 0.1980 chunk 189 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN G 201 GLN ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22406 Z= 0.214 Angle : 0.495 5.930 30563 Z= 0.266 Chirality : 0.040 0.141 3554 Planarity : 0.003 0.039 3666 Dihedral : 14.798 172.024 3437 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.43 % Allowed : 18.94 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.17), residues: 2584 helix: 2.03 (0.15), residues: 1233 sheet: 0.49 (0.22), residues: 529 loop : 0.23 (0.22), residues: 822 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 184 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 30 residues processed: 231 average time/residue: 3.1918 time to fit residues: 839.4081 Evaluate side-chains 198 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 3.287 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 0.5920 time to fit residues: 6.1448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 9.9990 chunk 177 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 ASN F 24 GLN F 255 ASN ** H 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22406 Z= 0.214 Angle : 0.493 5.935 30563 Z= 0.266 Chirality : 0.039 0.138 3554 Planarity : 0.003 0.040 3666 Dihedral : 14.776 167.350 3437 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.34 % Allowed : 19.07 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.17), residues: 2584 helix: 2.04 (0.15), residues: 1228 sheet: 0.48 (0.22), residues: 530 loop : 0.21 (0.22), residues: 826 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 173 time to evaluate : 3.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 32 residues processed: 219 average time/residue: 3.3281 time to fit residues: 830.9469 Evaluate side-chains 201 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 3.522 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 0.5776 time to fit residues: 6.4137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 187 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN A 571 ASN B 296 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 ASN G 201 GLN H 153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22406 Z= 0.231 Angle : 0.499 5.929 30563 Z= 0.268 Chirality : 0.040 0.134 3554 Planarity : 0.004 0.050 3666 Dihedral : 14.756 167.579 3437 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.30 % Allowed : 18.99 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.17), residues: 2584 helix: 2.02 (0.15), residues: 1227 sheet: 0.49 (0.22), residues: 527 loop : 0.20 (0.22), residues: 830 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 177 time to evaluate : 3.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 37 residues processed: 223 average time/residue: 3.1629 time to fit residues: 803.0413 Evaluate side-chains 206 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 169 time to evaluate : 3.411 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 34 residues processed: 3 average time/residue: 1.0314 time to fit residues: 8.6243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22406 Z= 0.200 Angle : 0.493 6.009 30563 Z= 0.264 Chirality : 0.039 0.134 3554 Planarity : 0.004 0.087 3666 Dihedral : 14.745 167.458 3437 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.99 % Allowed : 19.38 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.17), residues: 2584 helix: 2.05 (0.15), residues: 1228 sheet: 0.50 (0.22), residues: 527 loop : 0.21 (0.22), residues: 829 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 37 residues processed: 215 average time/residue: 3.2920 time to fit residues: 801.5208 Evaluate side-chains 207 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 170 time to evaluate : 3.381 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 35 residues processed: 2 average time/residue: 0.5064 time to fit residues: 6.1581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 211 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22406 Z= 0.253 Angle : 0.506 6.581 30563 Z= 0.272 Chirality : 0.040 0.139 3554 Planarity : 0.004 0.077 3666 Dihedral : 14.761 167.664 3437 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.04 % Allowed : 19.25 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.17), residues: 2584 helix: 1.98 (0.15), residues: 1227 sheet: 0.49 (0.22), residues: 526 loop : 0.16 (0.22), residues: 831 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 169 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 35 residues processed: 213 average time/residue: 3.2602 time to fit residues: 792.2843 Evaluate side-chains 200 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 3.356 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 35 residues processed: 0 time to fit residues: 4.1943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 170 optimal weight: 0.1980 chunk 123 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN G 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22406 Z= 0.192 Angle : 0.494 6.405 30563 Z= 0.264 Chirality : 0.039 0.146 3554 Planarity : 0.004 0.103 3666 Dihedral : 14.741 167.067 3437 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.86 % Allowed : 19.59 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.17), residues: 2584 helix: 2.03 (0.15), residues: 1229 sheet: 0.49 (0.22), residues: 528 loop : 0.19 (0.22), residues: 827 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 35 residues processed: 210 average time/residue: 3.2191 time to fit residues: 768.5678 Evaluate side-chains 200 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 3.288 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 35 residues processed: 0 time to fit residues: 4.1207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 140 optimal weight: 0.3980 chunk 101 optimal weight: 0.0050 chunk 183 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 220 optimal weight: 0.1980 chunk 232 optimal weight: 4.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN F 84 ASN G 201 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22406 Z= 0.166 Angle : 0.487 6.292 30563 Z= 0.260 Chirality : 0.039 0.137 3554 Planarity : 0.003 0.081 3666 Dihedral : 14.709 166.892 3437 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.86 % Allowed : 19.64 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.17), residues: 2584 helix: 2.11 (0.15), residues: 1230 sheet: 0.50 (0.22), residues: 526 loop : 0.22 (0.22), residues: 828 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 173 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 37 residues processed: 211 average time/residue: 3.1847 time to fit residues: 765.0652 Evaluate side-chains 205 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 168 time to evaluate : 3.305 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 35 residues processed: 2 average time/residue: 1.4725 time to fit residues: 7.8496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.5980 chunk 246 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 171 optimal weight: 0.7980 chunk 259 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN F 58 GLN G 24 GLN G 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22406 Z= 0.194 Angle : 0.498 7.786 30563 Z= 0.264 Chirality : 0.039 0.136 3554 Planarity : 0.003 0.088 3666 Dihedral : 14.709 167.351 3437 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.78 % Allowed : 19.77 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.17), residues: 2584 helix: 2.11 (0.15), residues: 1229 sheet: 0.52 (0.22), residues: 528 loop : 0.22 (0.22), residues: 827 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 60 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 37 residues processed: 205 average time/residue: 3.2667 time to fit residues: 765.4373 Evaluate side-chains 200 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 163 time to evaluate : 3.409 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 37 residues processed: 0 time to fit residues: 4.5876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 190 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 212 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 124 HIS G 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.110299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.068219 restraints weight = 92751.636| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.28 r_work: 0.2764 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2616 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: