Starting phenix.real_space_refine on Sun Mar 24 17:40:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqx_27663/03_2024/8dqx_27663_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqx_27663/03_2024/8dqx_27663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqx_27663/03_2024/8dqx_27663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqx_27663/03_2024/8dqx_27663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqx_27663/03_2024/8dqx_27663_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqx_27663/03_2024/8dqx_27663_trim.pdb" } resolution = 2.1 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= 0.051 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 39 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 13291 2.51 5 N 3595 2.21 5 O 5000 1.98 5 H 21143 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 369": "OE1" <-> "OE2" Residue "A TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A ASP 472": "OD1" <-> "OD2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A ASP 566": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 165": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43173 Number of models: 1 Model: "" Number of chains: 26 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: 5039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5039 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "C" Number of atoms: 5254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5254 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: 5685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5685 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 338} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 4046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4046 Classifications: {'peptide': 257} Modifications used: {'NH3': 1} 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: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 4039 Classifications: {'peptide': 256} Modifications used: {'NH3': 1} 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: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 191 Classifications: {'DNA': 6} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 5} Chain: "J" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 318 Classifications: {'DNA': 10} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 9} Chain: "K" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 318 Classifications: {'DNA': 10} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 9} 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} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Classifications: {'water': 126} Link IDs: {None: 125} Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 150 Classifications: {'water': 150} Link IDs: {None: 149} Chain: "C" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 156 Classifications: {'water': 156} Link IDs: {None: 155} Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 182 Classifications: {'water': 182} Link IDs: {None: 181} Chain: "E" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 170 Classifications: {'water': 170} Link IDs: {None: 169} Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 18.94, per 1000 atoms: 0.44 Number of scatterers: 43173 At special positions: 0 Unit cell: (126.378, 120.596, 142.898, 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 39 15.00 Mg 4 11.99 O 5000 8.00 N 3595 7.00 C 13291 6.00 H 21143 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: 36.94 Conformation dependent library (CDL) restraints added in 4.2 seconds 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4940 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 15 sheets defined 56.4% alpha, 15.4% beta 4 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 19.16 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 306 through 310 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.616A pdb=" N ASN A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.848A pdb=" N ARG A 434 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 460 through 467 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.660A pdb=" N ILE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 removed outlier: 3.920A pdb=" N ILE A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ARG A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 525 Processing helix chain 'A' and resid 535 through 543 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 584 removed outlier: 4.084A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) 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 657 Processing helix chain 'A' and resid 668 through 691 Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 704 through 714 removed outlier: 4.350A pdb=" N THR A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 removed outlier: 3.518A pdb=" N LEU A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 738 through 748 removed outlier: 3.542A pdb=" N PHE A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 754 Proline residue: A 752 - end of helix No H-bonds generated for 'chain 'A' and resid 749 through 754' 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 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: 4.108A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.836A 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 126 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.581A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) 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 217 Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.843A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.530A 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 257 through 260 Processing helix chain 'B' and resid 262 through 276 removed outlier: 3.535A pdb=" N ASN B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.504A 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 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 4.803A pdb=" N SER C 76 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 73 through 77' Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.600A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.582A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.609A pdb=" N CYS C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.858A 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: 4.012A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.066A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.845A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 3.826A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) 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: 4.379A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.455A 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: 4.898A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 4.057A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.772A 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 141 through 145 Processing helix chain 'D' and resid 146 through 160 removed outlier: 3.703A pdb=" N ARG D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (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 193 through 208 removed outlier: 3.671A pdb=" N ILE D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 225 removed outlier: 3.503A pdb=" N ALA D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) 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: 3.787A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 removed outlier: 3.529A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.574A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (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 removed outlier: 3.568A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.351A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 removed outlier: 3.536A pdb=" N LEU E 36 " --> pdb=" O PRO E 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 36' Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 63 through 67 Processing helix chain 'E' and resid 97 through 103 removed outlier: 6.891A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 removed outlier: 3.813A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.679A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 226 removed outlier: 3.501A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 337 through 353 removed outlier: 3.932A 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 19 through 23 removed outlier: 3.600A pdb=" N VAL F 23 " --> pdb=" O LYS F 20 " (cutoff:3.500A) 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 82 removed outlier: 3.567A pdb=" N GLY F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.692A 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: 3.681A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 20 removed outlier: 3.898A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 23 No H-bonds generated for 'chain 'G' and resid 21 through 23' 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 81 Processing helix chain 'G' and resid 141 through 155 removed outlier: 4.074A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER G 155 " --> pdb=" O LEU G 151 " (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: 3.966A pdb=" N SER G 220 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 20 removed outlier: 4.086A pdb=" N PHE H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 82 Processing helix chain 'H' and resid 141 through 153 removed outlier: 3.659A 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 216 Processing helix chain 'H' and resid 217 through 221 removed outlier: 4.087A pdb=" N SER H 220 " --> pdb=" O LYS H 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 377 removed outlier: 6.520A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 349 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N CYS A 455 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 351 " --> pdb=" O CYS A 455 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ALA A 348 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE A 473 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N MET A 350 " --> pdb=" O ILE A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.633A 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 Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.382A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.356A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 76 removed outlier: 6.536A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.431A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.719A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE F 111 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.582A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 6.119A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU G 59 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.615A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 176 through 182 removed outlier: 4.751A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 57 through 62 removed outlier: 4.204A pdb=" N LEU H 88 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU H 104 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 71 removed outlier: 7.599A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN H 38 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE H 36 " --> pdb=" O GLN H 29 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) 1156 hydrogen bonds defined for protein. 3219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 17.54 Time building geometry restraints manager: 38.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 21104 1.06 - 1.27: 3584 1.27 - 1.49: 8513 1.49 - 1.71: 9341 1.71 - 1.92: 159 Bond restraints: 42701 Sorted by residual: 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 4.94e+02 bond pdb=" C2' AGS A 901 " pdb=" C3' AGS A 901 " ideal model delta sigma weight residual 1.530 1.241 0.289 1.30e-02 5.92e+03 4.93e+02 bond pdb=" C2' AGS D 402 " pdb=" C3' AGS D 402 " ideal model delta sigma weight residual 1.530 1.245 0.285 1.30e-02 5.92e+03 4.81e+02 bond pdb=" C2' AGS C 402 " pdb=" C3' AGS C 402 " ideal model delta sigma weight residual 1.530 1.245 0.285 1.30e-02 5.92e+03 4.79e+02 bond pdb=" C6 AGS D 402 " pdb=" N6 AGS D 402 " ideal model delta sigma weight residual 1.335 1.466 -0.131 1.00e-02 1.00e+04 1.73e+02 ... (remaining 42696 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.08: 497 106.08 - 113.06: 51456 113.06 - 120.04: 12474 120.04 - 127.02: 12819 127.02 - 134.00: 232 Bond angle restraints: 77478 Sorted by residual: angle pdb=" C5 AGS C 402 " pdb=" C4 AGS C 402 " pdb=" N3 AGS C 402 " ideal model delta sigma weight residual 126.80 119.06 7.74 7.41e-01 1.82e+00 1.09e+02 angle pdb=" C5 AGS B 402 " pdb=" N7 AGS B 402 " pdb=" C8 AGS B 402 " ideal model delta sigma weight residual 103.67 108.12 -4.45 4.26e-01 5.51e+00 1.09e+02 angle pdb=" N1 AGS B 402 " pdb=" C2 AGS B 402 " pdb=" N3 AGS B 402 " ideal model delta sigma weight residual 128.80 120.09 8.71 8.41e-01 1.41e+00 1.07e+02 angle pdb=" C5 AGS A 901 " pdb=" N7 AGS A 901 " pdb=" C8 AGS A 901 " ideal model delta sigma weight residual 103.67 108.04 -4.37 4.26e-01 5.51e+00 1.05e+02 angle pdb=" C5 AGS D 402 " pdb=" N7 AGS D 402 " pdb=" C8 AGS D 402 " ideal model delta sigma weight residual 103.67 108.03 -4.36 4.26e-01 5.51e+00 1.05e+02 ... (remaining 77473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.27: 18548 26.27 - 52.54: 1034 52.54 - 78.82: 186 78.82 - 105.09: 24 105.09 - 131.36: 3 Dihedral angle restraints: 19795 sinusoidal: 11185 harmonic: 8610 Sorted by residual: 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 -76.01 -104.01 1 2.00e+01 2.50e-03 2.98e+01 dihedral pdb=" CA PHE A 419 " pdb=" C PHE A 419 " pdb=" N VAL A 420 " pdb=" CA VAL A 420 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLN D 25 " pdb=" C GLN D 25 " pdb=" N PRO D 26 " pdb=" CA PRO D 26 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 19792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2942 0.060 - 0.120: 404 0.120 - 0.179: 50 0.179 - 0.239: 5 0.239 - 0.299: 4 Chirality restraints: 3405 Sorted by residual: 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 -2.38 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' AGS A 901 " pdb=" C1' AGS A 901 " pdb=" C3' AGS A 901 " pdb=" O2' AGS A 901 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2' AGS D 402 " pdb=" C1' AGS D 402 " pdb=" C3' AGS D 402 " pdb=" O2' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.40 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 3402 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 61 " -0.198 9.50e-02 1.11e+02 6.62e-02 5.31e+00 pdb=" NE ARG G 61 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG G 61 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 61 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 61 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG G 61 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG G 61 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG G 61 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG G 61 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 95 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C ASN C 95 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN C 95 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN C 96 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC K 5 " 0.019 2.00e-02 2.50e+03 9.66e-03 2.57e+00 pdb=" N1 DC K 5 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DC K 5 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC K 5 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DC K 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC K 5 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC K 5 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DC K 5 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC K 5 " -0.002 2.00e-02 2.50e+03 pdb=" H5 DC K 5 " 0.003 2.00e-02 2.50e+03 pdb=" H6 DC K 5 " -0.001 2.00e-02 2.50e+03 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 890 2.09 - 2.71: 71710 2.71 - 3.34: 130379 3.34 - 3.97: 171462 3.97 - 4.60: 264335 Nonbonded interactions: 638776 Sorted by model distance: nonbonded pdb=" OE1 GLU B 169 " pdb=" H GLU B 169 " model vdw 1.457 1.850 nonbonded pdb=" OE1 GLU F 55 " pdb=" H GLU F 55 " model vdw 1.490 1.850 nonbonded pdb="HH12 ARG C 267 " pdb=" OD2 ASP C 316 " model vdw 1.528 1.850 nonbonded pdb=" OE1 GLU G 8 " pdb=" H GLU G 8 " model vdw 1.528 1.850 nonbonded pdb=" HZ3 LYS B 100 " pdb=" OD1 ASP G 120 " model vdw 1.584 1.850 ... (remaining 638771 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.740 Extract box with map and model: 13.890 Check model and map are aligned: 0.620 Set scattering table: 0.380 Process input model: 150.310 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.110 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:14.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 186.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 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 0.289 21558 Z= 0.542 Angle : 0.681 9.127 29260 Z= 0.439 Chirality : 0.043 0.299 3405 Planarity : 0.004 0.087 3628 Dihedral : 17.316 131.359 8241 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.26 % Allowed : 16.41 % Favored : 82.34 % 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: 1.11 (0.16), residues: 2582 helix: 1.13 (0.15), residues: 1204 sheet: 0.64 (0.21), residues: 536 loop : 0.45 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 669 HIS 0.010 0.002 HIS B 216 PHE 0.025 0.002 PHE A 585 TYR 0.017 0.002 TYR A 688 ARG 0.012 0.001 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 313 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 119 MET cc_start: 0.7425 (mmp) cc_final: 0.7126 (mmp) outliers start: 29 outliers final: 8 residues processed: 337 average time/residue: 3.7745 time to fit residues: 1410.4576 Evaluate side-chains 185 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 3.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 97 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 234 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS E 32 GLN F 255 ASN G 24 GLN G 84 ASN H 58 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21558 Z= 0.232 Angle : 0.550 6.245 29260 Z= 0.295 Chirality : 0.041 0.147 3405 Planarity : 0.004 0.058 3628 Dihedral : 12.334 139.062 3148 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.78 % Allowed : 16.36 % Favored : 81.86 % 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: 1.45 (0.17), residues: 2582 helix: 1.48 (0.15), residues: 1237 sheet: 0.82 (0.22), residues: 537 loop : 0.46 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 669 HIS 0.007 0.001 HIS B 232 PHE 0.012 0.001 PHE E 328 TYR 0.011 0.001 TYR A 688 ARG 0.007 0.000 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6408 (tt0) REVERT: H 83 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.7191 (t0) outliers start: 41 outliers final: 11 residues processed: 219 average time/residue: 3.6857 time to fit residues: 899.8850 Evaluate side-chains 184 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 398 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN F 255 ASN G 24 GLN G 84 ASN H 83 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21558 Z= 0.301 Angle : 0.550 6.126 29260 Z= 0.293 Chirality : 0.042 0.145 3405 Planarity : 0.004 0.047 3628 Dihedral : 12.117 131.780 3141 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.56 % Allowed : 15.54 % Favored : 82.90 % 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: 1.52 (0.17), residues: 2582 helix: 1.62 (0.15), residues: 1226 sheet: 0.86 (0.22), residues: 535 loop : 0.33 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 324 HIS 0.008 0.001 HIS B 232 PHE 0.015 0.001 PHE E 328 TYR 0.013 0.002 TYR D 160 ARG 0.005 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 180 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: E 120 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6183 (mt-10) outliers start: 36 outliers final: 17 residues processed: 210 average time/residue: 3.6270 time to fit residues: 852.2370 Evaluate side-chains 191 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 249 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN D 24 GLN F 255 ASN G 24 GLN G 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21558 Z= 0.250 Angle : 0.520 5.983 29260 Z= 0.278 Chirality : 0.040 0.143 3405 Planarity : 0.004 0.041 3628 Dihedral : 11.986 133.679 3139 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.35 % Allowed : 15.36 % Favored : 83.29 % 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: 1.59 (0.17), residues: 2582 helix: 1.73 (0.15), residues: 1233 sheet: 0.90 (0.22), residues: 535 loop : 0.25 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 324 HIS 0.006 0.001 HIS B 232 PHE 0.013 0.001 PHE F 185 TYR 0.012 0.001 TYR D 160 ARG 0.005 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6411 (tt0) outliers start: 31 outliers final: 15 residues processed: 203 average time/residue: 3.7379 time to fit residues: 845.2567 Evaluate side-chains 187 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 212 optimal weight: 0.1980 chunk 172 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 408 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN D 24 GLN F 255 ASN G 24 GLN G 84 ASN H 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21558 Z= 0.290 Angle : 0.527 7.152 29260 Z= 0.282 Chirality : 0.041 0.149 3405 Planarity : 0.004 0.039 3628 Dihedral : 11.981 133.222 3139 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.48 % Allowed : 15.23 % Favored : 83.29 % 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: 1.62 (0.17), residues: 2582 helix: 1.76 (0.15), residues: 1227 sheet: 0.90 (0.22), residues: 533 loop : 0.28 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 324 HIS 0.007 0.001 HIS B 232 PHE 0.015 0.001 PHE E 328 TYR 0.012 0.001 TYR D 160 ARG 0.008 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6434 (tt0) REVERT: E 120 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6432 (mt-10) outliers start: 34 outliers final: 20 residues processed: 200 average time/residue: 3.5701 time to fit residues: 799.4697 Evaluate side-chains 187 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 0.1980 chunk 131 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 408 ASN D 24 GLN G 24 GLN H 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21558 Z= 0.172 Angle : 0.491 6.275 29260 Z= 0.261 Chirality : 0.039 0.143 3405 Planarity : 0.003 0.039 3628 Dihedral : 11.856 133.726 3139 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.09 % Allowed : 15.89 % Favored : 83.03 % 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: 2582 helix: 1.87 (0.15), residues: 1244 sheet: 0.98 (0.22), residues: 530 loop : 0.27 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 324 HIS 0.005 0.001 HIS E 292 PHE 0.014 0.001 PHE F 185 TYR 0.010 0.001 TYR D 160 ARG 0.008 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 171 time to evaluate : 3.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: B 203 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7556 (ttm170) outliers start: 25 outliers final: 16 residues processed: 189 average time/residue: 3.6068 time to fit residues: 762.9867 Evaluate side-chains 186 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 408 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN F 84 ASN G 24 GLN H 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21558 Z= 0.227 Angle : 0.503 7.324 29260 Z= 0.267 Chirality : 0.040 0.140 3405 Planarity : 0.003 0.040 3628 Dihedral : 11.843 133.893 3139 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.13 % Allowed : 15.93 % Favored : 82.94 % 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: 1.76 (0.17), residues: 2582 helix: 1.91 (0.15), residues: 1234 sheet: 0.98 (0.22), residues: 527 loop : 0.26 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 324 HIS 0.006 0.001 HIS B 232 PHE 0.013 0.001 PHE E 328 TYR 0.012 0.001 TYR D 160 ARG 0.006 0.000 ARG G 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 3.165 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: B 77 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6416 (tt0) REVERT: B 203 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7564 (ttm170) outliers start: 26 outliers final: 15 residues processed: 189 average time/residue: 3.6939 time to fit residues: 778.5083 Evaluate side-chains 181 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 158 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 408 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN G 24 GLN H 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21558 Z= 0.242 Angle : 0.513 9.160 29260 Z= 0.271 Chirality : 0.040 0.140 3405 Planarity : 0.003 0.040 3628 Dihedral : 11.836 133.499 3139 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.09 % Allowed : 15.89 % Favored : 83.03 % 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: 1.77 (0.17), residues: 2582 helix: 1.91 (0.15), residues: 1234 sheet: 0.98 (0.22), residues: 531 loop : 0.29 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 324 HIS 0.006 0.001 HIS B 232 PHE 0.014 0.001 PHE E 328 TYR 0.012 0.001 TYR D 160 ARG 0.006 0.000 ARG G 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 175 time to evaluate : 3.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6414 (tt0) REVERT: B 203 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7570 (ttm170) outliers start: 25 outliers final: 16 residues processed: 196 average time/residue: 3.7252 time to fit residues: 819.2238 Evaluate side-chains 183 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 209 optimal weight: 0.8980 chunk 219 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 408 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN G 24 GLN H 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21558 Z= 0.252 Angle : 0.524 10.301 29260 Z= 0.276 Chirality : 0.040 0.142 3405 Planarity : 0.003 0.039 3628 Dihedral : 11.831 133.595 3139 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.09 % Allowed : 15.89 % Favored : 83.03 % 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: 1.78 (0.17), residues: 2582 helix: 1.91 (0.15), residues: 1233 sheet: 1.02 (0.22), residues: 531 loop : 0.28 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 324 HIS 0.007 0.001 HIS B 232 PHE 0.014 0.001 PHE E 328 TYR 0.012 0.001 TYR D 160 ARG 0.008 0.000 ARG G 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 4.142 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 77 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6417 (tt0) REVERT: B 203 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7582 (ttm170) outliers start: 25 outliers final: 18 residues processed: 192 average time/residue: 3.7430 time to fit residues: 800.7263 Evaluate side-chains 180 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 chunk 158 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 398 ASN A 408 ASN G 24 GLN H 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21558 Z= 0.187 Angle : 0.503 10.932 29260 Z= 0.265 Chirality : 0.039 0.141 3405 Planarity : 0.003 0.039 3628 Dihedral : 11.764 134.008 3139 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.04 % Allowed : 16.06 % Favored : 82.90 % 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: 1.86 (0.17), residues: 2582 helix: 1.98 (0.15), residues: 1240 sheet: 0.99 (0.22), residues: 531 loop : 0.36 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 324 HIS 0.005 0.001 HIS B 232 PHE 0.011 0.001 PHE F 185 TYR 0.011 0.001 TYR D 160 ARG 0.008 0.000 ARG G 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 360 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 3.811 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 77 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6408 (tt0) REVERT: B 203 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7563 (ttm170) outliers start: 24 outliers final: 18 residues processed: 185 average time/residue: 3.5440 time to fit residues: 734.9109 Evaluate side-chains 186 residues out of total 2309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 398 ASN A 408 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN G 24 GLN H 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.054514 restraints weight = 95482.069| |-----------------------------------------------------------------------------| r_work (start): 0.2583 rms_B_bonded: 2.32 r_work: 0.2452 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2322 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21558 Z= 0.166 Angle : 0.496 10.805 29260 Z= 0.260 Chirality : 0.039 0.142 3405 Planarity : 0.003 0.039 3628 Dihedral : 11.685 134.384 3139 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.00 % Allowed : 16.15 % Favored : 82.86 % 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: 1.95 (0.17), residues: 2582 helix: 2.05 (0.15), residues: 1248 sheet: 1.05 (0.22), residues: 530 loop : 0.35 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 324 HIS 0.004 0.001 HIS B 232 PHE 0.011 0.001 PHE F 185 TYR 0.009 0.001 TYR D 160 ARG 0.006 0.000 ARG A 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15967.51 seconds wall clock time: 279 minutes 7.32 seconds (16747.32 seconds total)