Starting phenix.real_space_refine on Sun Mar 24 16:58:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr7_27673/03_2024/8dr7_27673_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr7_27673/03_2024/8dr7_27673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr7_27673/03_2024/8dr7_27673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr7_27673/03_2024/8dr7_27673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr7_27673/03_2024/8dr7_27673_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr7_27673/03_2024/8dr7_27673_trim.pdb" } resolution = 2.7 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= 0.038 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 63 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 13516 2.51 5 N 3694 2.21 5 O 4277 1.98 5 H 21405 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 376": "OE1" <-> "OE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A ASP 704": "OD1" <-> "OD2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A ASP 734": "OD1" <-> "OD2" Residue "A TYR 735": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 747": "OE1" <-> "OE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C ASP 225": "OD1" <-> "OD2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "D ASP 312": "OD1" <-> "OD2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E GLU 302": "OE1" <-> "OE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ASP 172": "OD1" <-> "OD2" Residue "F PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F ASP 223": "OD1" <-> "OD2" Residue "F ASP 240": "OD1" <-> "OD2" Residue "F PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G ASP 105": "OD1" <-> "OD2" Residue "G ASP 109": "OD1" <-> "OD2" Residue "G ASP 120": "OD1" <-> "OD2" Residue "G ASP 124": "OD1" <-> "OD2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "G ASP 200": "OD1" <-> "OD2" Residue "G ASP 223": "OD1" <-> "OD2" Residue "G PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 43060 Number of models: 1 Model: "" Number of chains: 16 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: 5083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5083 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} 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: 5675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5675 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "F" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4044 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 4037 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 4060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4060 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 814 Classifications: {'DNA': 26} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 25} Chain: "J" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 373 Classifications: {'DNA': 12} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 11} Chain: "K" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 363 Classifications: {'DNA': 11} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.91, per 1000 atoms: 0.44 Number of scatterers: 43060 At special positions: 0 Unit cell: (132.16, 120.596, 144.55, 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 63 15.00 Mg 4 11.99 O 4277 8.00 N 3694 7.00 C 13516 6.00 H 21405 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: 29.83 Conformation dependent library (CDL) restraints added in 3.8 seconds 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 17 sheets defined 54.0% alpha, 14.8% beta 11 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 19.85 Creating SS restraints... 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 Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.669A pdb=" N ALA A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 removed outlier: 4.326A pdb=" N ALA A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 435 through 444 removed outlier: 3.524A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 467 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 483 through 495 Processing helix chain 'A' and resid 502 through 511 removed outlier: 3.758A pdb=" N LEU A 506 " --> pdb=" O VAL A 502 " (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 565 through 572 removed outlier: 3.846A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 4.152A 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 656 removed outlier: 3.528A pdb=" N LYS A 655 " --> pdb=" O TYR A 651 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 656 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 690 Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 704 through 714 removed outlier: 4.132A pdb=" N THR A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 718 Processing helix chain 'A' and resid 720 through 723 Processing helix chain 'A' and resid 724 through 736 Processing helix chain 'A' and resid 738 through 749 removed outlier: 4.295A pdb=" N PHE A 749 " --> pdb=" O ILE A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.624A pdb=" N VAL A 754 " --> pdb=" O GLY A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 763 through 776 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.571A pdb=" N ILE B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.855A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.657A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.598A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 215 removed outlier: 4.482A pdb=" N VAL B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.828A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.740A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.541A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.526A pdb=" N ASN C 12 " --> pdb=" O SER C 9 " (cutoff:3.500A) 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 43 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.891A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.591A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.619A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.512A pdb=" N ARG C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.701A 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 221 through 224 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 3.974A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.037A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 4.272A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 3.750A 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 removed outlier: 3.629A pdb=" N GLU D 38 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 35 through 39' Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.361A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.774A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.310A 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 152 removed outlier: 3.575A pdb=" N ALA D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.649A 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 197 through 208 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.671A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 296 through 311 Processing helix chain 'D' and resid 315 through 334 removed outlier: 3.671A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 removed outlier: 3.525A pdb=" N GLN D 342 " --> pdb=" O ASN D 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.589A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.286A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 97 through 103 removed outlier: 7.056A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.909A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 4.303A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR E 161 " --> pdb=" O THR E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 257 through 273 removed outlier: 3.588A pdb=" N LYS E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.829A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 353 removed outlier: 3.815A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY E 344 " --> pdb=" O PHE E 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.912A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE F 15 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.613A 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 221 removed outlier: 4.324A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 19 removed outlier: 4.306A pdb=" N PHE G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 82 removed outlier: 3.503A pdb=" N GLY G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.752A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 221 removed outlier: 4.401A pdb=" N SER G 220 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 18 removed outlier: 3.868A pdb=" N PHE H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 81 removed outlier: 4.131A pdb=" N CYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 153 removed outlier: 3.643A pdb=" N ASP H 150 " --> pdb=" O LYS H 146 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 218 Processing helix chain 'H' and resid 219 through 221 No H-bonds generated for 'chain 'H' and resid 219 through 221' Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 377 removed outlier: 8.741A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA A 348 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE A 473 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N MET A 350 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.768A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 601 removed outlier: 3.566A pdb=" N HIS A 659 " --> pdb=" O ARG A 600 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.349A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.379A 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 removed outlier: 6.460A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.130A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.549A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.836A pdb=" N VAL E 170 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.836A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 57 through 62 removed outlier: 3.755A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE F 111 " --> pdb=" O ILE H 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.722A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 203 through 208 removed outlier: 5.752A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE G 111 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU G 59 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.232A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER G 138 " --> pdb=" O LYS G 196 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS G 196 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 179 through 182 Processing sheet with id=AB6, first strand: chain 'H' and resid 2 through 6 Processing sheet with id=AB7, first strand: chain 'H' and resid 66 through 68 removed outlier: 4.035A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 89 through 91 1118 hydrogen bonds defined for protein. 3153 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 17.56 Time building geometry restraints manager: 31.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 21366 1.05 - 1.27: 3608 1.27 - 1.49: 8669 1.49 - 1.70: 9710 1.70 - 1.92: 159 Bond restraints: 43512 Sorted by residual: bond pdb=" C2' AGS D 402 " pdb=" C3' AGS D 402 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.00e+02 bond pdb=" C2' AGS B 403 " pdb=" C3' AGS B 403 " ideal model delta sigma weight residual 1.530 1.240 0.290 1.30e-02 5.92e+03 4.98e+02 bond pdb=" C2' AGS C 402 " pdb=" C3' AGS C 402 " ideal model delta sigma weight residual 1.530 1.240 0.290 1.30e-02 5.92e+03 4.98e+02 bond pdb=" C2' AGS A1001 " pdb=" C3' AGS A1001 " ideal model delta sigma weight residual 1.530 1.241 0.289 1.30e-02 5.92e+03 4.94e+02 bond pdb=" C6 AGS D 402 " pdb=" N6 AGS D 402 " ideal model delta sigma weight residual 1.335 1.469 -0.134 1.00e-02 1.00e+04 1.78e+02 ... (remaining 43507 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.74: 893 106.74 - 113.55: 52772 113.55 - 120.35: 13618 120.35 - 127.16: 11399 127.16 - 133.97: 254 Bond angle restraints: 78936 Sorted by residual: angle pdb=" N1 AGS A1001 " pdb=" C2 AGS A1001 " pdb=" N3 AGS A1001 " ideal model delta sigma weight residual 128.80 120.04 8.76 8.41e-01 1.41e+00 1.08e+02 angle pdb=" N1 AGS B 403 " pdb=" C2 AGS B 403 " pdb=" N3 AGS B 403 " ideal model delta sigma weight residual 128.80 120.08 8.72 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS D 402 " pdb=" C2 AGS D 402 " pdb=" N3 AGS D 402 " ideal model delta sigma weight residual 128.80 120.09 8.71 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS C 402 " pdb=" C2 AGS C 402 " pdb=" N3 AGS C 402 " ideal model delta sigma weight residual 128.80 120.15 8.65 8.41e-01 1.41e+00 1.06e+02 angle pdb=" C5 AGS D 402 " pdb=" N7 AGS D 402 " pdb=" C8 AGS D 402 " ideal model delta sigma weight residual 103.67 107.99 -4.32 4.26e-01 5.51e+00 1.03e+02 ... (remaining 78931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.79: 18745 26.79 - 53.58: 1132 53.58 - 80.37: 160 80.37 - 107.16: 9 107.16 - 133.96: 4 Dihedral angle restraints: 20050 sinusoidal: 11435 harmonic: 8615 Sorted by residual: dihedral pdb=" O2B GDP E 401 " pdb=" O3A GDP E 401 " pdb=" PB GDP E 401 " pdb=" PA GDP E 401 " ideal model delta sinusoidal sigma weight residual 180.00 46.04 133.96 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" O1A AGS C 402 " pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sinusoidal sigma weight residual -67.73 64.62 -132.35 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" O1A AGS D 402 " pdb=" O3A AGS D 402 " pdb=" PA AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sinusoidal sigma weight residual -67.73 64.48 -132.21 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 20047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3079 0.061 - 0.123: 384 0.123 - 0.184: 31 0.184 - 0.245: 4 0.245 - 0.306: 4 Chirality restraints: 3502 Sorted by residual: 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 -2.37 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' AGS C 402 " pdb=" C1' AGS C 402 " pdb=" C3' AGS C 402 " pdb=" O2' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.37 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C2' AGS B 403 " pdb=" C1' AGS B 403 " pdb=" C3' AGS B 403 " pdb=" O2' AGS B 403 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 3499 not shown) Planarity restraints: 6198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 511 " -0.252 9.50e-02 1.11e+02 8.45e-02 8.52e+00 pdb=" NE ARG A 511 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 511 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 511 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 511 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 511 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 511 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 511 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 511 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 14 " -0.235 9.50e-02 1.11e+02 7.87e-02 7.81e+00 pdb=" NE ARG G 14 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG G 14 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG G 14 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 14 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG G 14 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG G 14 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG G 14 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG G 14 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " -0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO E 63 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " -0.035 5.00e-02 4.00e+02 ... (remaining 6195 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 782 2.09 - 2.72: 72464 2.72 - 3.35: 124569 3.35 - 3.97: 161345 3.97 - 4.60: 251574 Nonbonded interactions: 610734 Sorted by model distance: nonbonded pdb=" OE1 GLU C 294 " pdb=" H GLU C 294 " model vdw 1.467 1.850 nonbonded pdb=" OE1 GLU F 32 " pdb=" H GLU F 32 " model vdw 1.478 1.850 nonbonded pdb=" OE1 GLU G 143 " pdb=" H GLU G 143 " model vdw 1.537 1.850 nonbonded pdb=" OE1 GLU H 189 " pdb=" H GLU H 189 " model vdw 1.544 1.850 nonbonded pdb=" OD1 ASN D 96 " pdb=" HG SER D 98 " model vdw 1.559 1.850 ... (remaining 610729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'F' and resid 1 through 255) selection = (chain 'G' and resid 1 through 255) selection = (chain 'H' and resid 1 through 255) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.620 Extract box with map and model: 14.160 Check model and map are aligned: 0.720 Set scattering table: 0.440 Process input model: 142.540 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.291 22107 Z= 0.397 Angle : 0.598 8.760 30104 Z= 0.399 Chirality : 0.041 0.306 3502 Planarity : 0.004 0.111 3653 Dihedral : 17.409 133.956 8466 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.91 % Allowed : 20.50 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.18), residues: 2584 helix: 2.27 (0.16), residues: 1188 sheet: 0.66 (0.23), residues: 511 loop : 0.33 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP E 259 HIS 0.006 0.000 HIS D 124 PHE 0.019 0.001 PHE G 245 TYR 0.007 0.001 TYR D 286 ARG 0.017 0.000 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 328 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 307 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 MET cc_start: 0.0170 (ptt) cc_final: -0.0376 (ptm) REVERT: H 161 MET cc_start: 0.7416 (mtp) cc_final: 0.6950 (tmt) REVERT: H 257 GLU cc_start: 0.5984 (pt0) cc_final: 0.5572 (pp20) outliers start: 21 outliers final: 10 residues processed: 325 average time/residue: 3.1850 time to fit residues: 1170.1029 Evaluate side-chains 208 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 198 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain H residue 174 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 236 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 91 ASN B 95 HIS E 80 ASN E 118 GLN E 243 ASN F 94 ASN G 27 ASN G 29 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22107 Z= 0.241 Angle : 0.538 6.934 30104 Z= 0.286 Chirality : 0.040 0.162 3502 Planarity : 0.004 0.063 3653 Dihedral : 13.548 156.009 3373 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.56 % Allowed : 20.46 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.17), residues: 2584 helix: 1.97 (0.16), residues: 1214 sheet: 0.57 (0.23), residues: 524 loop : 0.16 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 638 HIS 0.004 0.001 HIS D 124 PHE 0.012 0.001 PHE E 328 TYR 0.010 0.001 TYR D 286 ARG 0.009 0.001 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 197 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8658 (mp10) REVERT: F 44 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8205 (mtt90) REVERT: G 245 PHE cc_start: 0.8211 (p90) cc_final: 0.7991 (p90) REVERT: H 3 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6151 (mp0) REVERT: H 70 MET cc_start: 0.0222 (ptt) cc_final: -0.0189 (ptm) REVERT: H 149 ARG cc_start: 0.8306 (ptm-80) cc_final: 0.7827 (ttp80) REVERT: H 161 MET cc_start: 0.7466 (mtp) cc_final: 0.6956 (tmt) outliers start: 59 outliers final: 22 residues processed: 246 average time/residue: 2.7424 time to fit residues: 784.5031 Evaluate side-chains 208 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 144 PHE Chi-restraints excluded: chain H residue 156 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.0070 chunk 73 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 236 optimal weight: 20.0000 chunk 255 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 GLN E 243 ASN F 94 ASN G 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22107 Z= 0.211 Angle : 0.499 6.767 30104 Z= 0.265 Chirality : 0.039 0.161 3502 Planarity : 0.004 0.052 3653 Dihedral : 13.557 163.837 3364 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.38 % Allowed : 19.38 % Favored : 78.24 % 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: 1.58 (0.17), residues: 2584 helix: 2.00 (0.16), residues: 1209 sheet: 0.55 (0.23), residues: 525 loop : 0.09 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 638 HIS 0.004 0.001 HIS D 124 PHE 0.012 0.001 PHE A 405 TYR 0.008 0.001 TYR D 286 ARG 0.006 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 3.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8648 (mp10) REVERT: F 44 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8193 (mtt90) REVERT: G 245 PHE cc_start: 0.8204 (p90) cc_final: 0.7969 (p90) REVERT: H 70 MET cc_start: 0.0022 (ptt) cc_final: -0.0288 (ptm) REVERT: H 149 ARG cc_start: 0.8310 (ptm-80) cc_final: 0.7514 (ttp80) REVERT: H 257 GLU cc_start: 0.5899 (pt0) cc_final: 0.5643 (pp20) outliers start: 55 outliers final: 22 residues processed: 241 average time/residue: 2.7913 time to fit residues: 773.8468 Evaluate side-chains 202 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 144 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 610 HIS B 146 GLN E 243 ASN F 94 ASN G 153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22107 Z= 0.286 Angle : 0.511 6.263 30104 Z= 0.274 Chirality : 0.040 0.153 3502 Planarity : 0.004 0.081 3653 Dihedral : 13.674 168.262 3364 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.47 % Allowed : 19.07 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.17), residues: 2584 helix: 1.92 (0.16), residues: 1203 sheet: 0.54 (0.23), residues: 519 loop : -0.02 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 638 HIS 0.005 0.001 HIS A 337 PHE 0.013 0.001 PHE E 328 TYR 0.010 0.001 TYR D 286 ARG 0.005 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 181 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8757 (mp10) REVERT: A 732 MET cc_start: 0.8925 (mtt) cc_final: 0.8512 (mtt) REVERT: B 77 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: G 245 PHE cc_start: 0.8229 (p90) cc_final: 0.7961 (p90) REVERT: H 70 MET cc_start: 0.0243 (ptt) cc_final: -0.0092 (ptm) REVERT: H 149 ARG cc_start: 0.8325 (ptm-80) cc_final: 0.7510 (ttp80) REVERT: H 161 MET cc_start: 0.7519 (ttp) cc_final: 0.6944 (tmt) REVERT: H 211 TYR cc_start: 0.7541 (m-80) cc_final: 0.5791 (t80) REVERT: H 257 GLU cc_start: 0.6050 (pt0) cc_final: 0.5724 (pp20) outliers start: 57 outliers final: 32 residues processed: 230 average time/residue: 2.7829 time to fit residues: 737.6118 Evaluate side-chains 207 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 3.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 144 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 5.9990 chunk 142 optimal weight: 0.0050 chunk 3 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 118 GLN F 94 ASN G 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22107 Z= 0.258 Angle : 0.505 6.196 30104 Z= 0.270 Chirality : 0.040 0.175 3502 Planarity : 0.004 0.053 3653 Dihedral : 13.701 168.442 3364 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.21 % Allowed : 19.68 % Favored : 78.11 % 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: 1.42 (0.17), residues: 2584 helix: 1.92 (0.15), residues: 1199 sheet: 0.47 (0.23), residues: 519 loop : -0.06 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 638 HIS 0.004 0.001 HIS E 18 PHE 0.012 0.001 PHE G 28 TYR 0.032 0.001 TYR G 133 ARG 0.005 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 176 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8746 (mp10) REVERT: A 732 MET cc_start: 0.8900 (mtt) cc_final: 0.8499 (mtt) REVERT: B 77 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: F 201 GLN cc_start: 0.8941 (mm110) cc_final: 0.8575 (mp10) REVERT: G 245 PHE cc_start: 0.8259 (p90) cc_final: 0.7968 (p90) REVERT: H 70 MET cc_start: 0.0279 (ptt) cc_final: 0.0055 (ptm) REVERT: H 149 ARG cc_start: 0.8318 (ptm-80) cc_final: 0.7506 (ttp80) REVERT: H 161 MET cc_start: 0.7520 (ttp) cc_final: 0.6891 (tmt) REVERT: H 211 TYR cc_start: 0.7537 (m-80) cc_final: 0.5767 (t80) REVERT: H 257 GLU cc_start: 0.5883 (pt0) cc_final: 0.5649 (pp20) outliers start: 51 outliers final: 33 residues processed: 220 average time/residue: 2.8910 time to fit residues: 737.2060 Evaluate side-chains 203 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 144 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 3.9990 chunk 226 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 chunk 208 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS B 148 ASN E 118 GLN F 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22107 Z= 0.244 Angle : 0.501 6.206 30104 Z= 0.268 Chirality : 0.040 0.161 3502 Planarity : 0.004 0.101 3653 Dihedral : 13.704 168.431 3364 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.38 % Allowed : 19.16 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.17), residues: 2584 helix: 1.91 (0.15), residues: 1203 sheet: 0.44 (0.23), residues: 519 loop : -0.06 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 638 HIS 0.006 0.001 HIS A 337 PHE 0.012 0.001 PHE E 328 TYR 0.021 0.001 TYR G 133 ARG 0.007 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 169 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8750 (mp10) REVERT: A 732 MET cc_start: 0.8900 (mtt) cc_final: 0.8529 (mtt) REVERT: B 77 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: F 84 ASN cc_start: 0.8909 (m-40) cc_final: 0.8663 (t0) REVERT: F 201 GLN cc_start: 0.8910 (mm110) cc_final: 0.8504 (mp10) REVERT: G 245 PHE cc_start: 0.8266 (p90) cc_final: 0.7950 (p90) REVERT: H 149 ARG cc_start: 0.8320 (ptm-80) cc_final: 0.7519 (ttp80) REVERT: H 161 MET cc_start: 0.7543 (ttp) cc_final: 0.6884 (tmt) REVERT: H 211 TYR cc_start: 0.7565 (m-80) cc_final: 0.5789 (t80) outliers start: 55 outliers final: 32 residues processed: 216 average time/residue: 2.9383 time to fit residues: 725.9952 Evaluate side-chains 201 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 43 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS D 25 GLN E 118 GLN F 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22107 Z= 0.259 Angle : 0.506 6.293 30104 Z= 0.271 Chirality : 0.040 0.153 3502 Planarity : 0.004 0.066 3653 Dihedral : 13.719 168.512 3364 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.43 % Allowed : 18.99 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2584 helix: 1.88 (0.15), residues: 1202 sheet: 0.38 (0.22), residues: 519 loop : -0.08 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 638 HIS 0.007 0.001 HIS A 337 PHE 0.012 0.001 PHE E 328 TYR 0.021 0.001 TYR G 133 ARG 0.009 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 167 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8719 (mp10) REVERT: A 732 MET cc_start: 0.8896 (mtt) cc_final: 0.8544 (mtt) REVERT: B 77 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: F 84 ASN cc_start: 0.8876 (m-40) cc_final: 0.8633 (t0) REVERT: G 245 PHE cc_start: 0.8291 (p90) cc_final: 0.7915 (p90) REVERT: H 149 ARG cc_start: 0.8297 (ptm-80) cc_final: 0.7489 (ttp80) REVERT: H 161 MET cc_start: 0.7508 (ttp) cc_final: 0.6830 (tmt) REVERT: H 211 TYR cc_start: 0.7571 (m-80) cc_final: 0.5797 (t80) outliers start: 56 outliers final: 34 residues processed: 211 average time/residue: 2.9599 time to fit residues: 712.5447 Evaluate side-chains 199 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 3.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 43 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 118 GLN F 94 ASN G 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22107 Z= 0.163 Angle : 0.490 6.134 30104 Z= 0.261 Chirality : 0.039 0.151 3502 Planarity : 0.004 0.106 3653 Dihedral : 13.676 168.180 3364 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.52 % Allowed : 20.20 % Favored : 78.28 % 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: 1.48 (0.17), residues: 2584 helix: 2.00 (0.15), residues: 1201 sheet: 0.40 (0.22), residues: 519 loop : -0.01 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 638 HIS 0.009 0.001 HIS A 337 PHE 0.010 0.001 PHE E 328 TYR 0.015 0.001 TYR A 404 ARG 0.012 0.000 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8704 (mp10) REVERT: A 732 MET cc_start: 0.8866 (mtt) cc_final: 0.8505 (mtt) REVERT: E 217 ASP cc_start: 0.7846 (t70) cc_final: 0.7619 (t0) REVERT: G 245 PHE cc_start: 0.8250 (p90) cc_final: 0.7876 (p90) REVERT: H 149 ARG cc_start: 0.8294 (ptm-80) cc_final: 0.7484 (ttp80) REVERT: H 161 MET cc_start: 0.7527 (ttp) cc_final: 0.6815 (tmt) REVERT: H 211 TYR cc_start: 0.7558 (m-80) cc_final: 0.5790 (t80) outliers start: 35 outliers final: 26 residues processed: 195 average time/residue: 3.1173 time to fit residues: 698.5265 Evaluate side-chains 191 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 86 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 118 GLN F 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22107 Z= 0.258 Angle : 0.507 8.924 30104 Z= 0.269 Chirality : 0.040 0.147 3502 Planarity : 0.004 0.068 3653 Dihedral : 13.682 168.286 3363 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.43 % Allowed : 20.33 % Favored : 78.24 % 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: 1.39 (0.17), residues: 2584 helix: 1.91 (0.15), residues: 1205 sheet: 0.38 (0.22), residues: 518 loop : -0.05 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 638 HIS 0.005 0.001 HIS B 232 PHE 0.012 0.001 PHE E 328 TYR 0.016 0.001 TYR G 133 ARG 0.010 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8711 (mp10) REVERT: A 732 MET cc_start: 0.8891 (mtt) cc_final: 0.8552 (mtt) REVERT: E 217 ASP cc_start: 0.7847 (t70) cc_final: 0.7616 (t0) REVERT: H 149 ARG cc_start: 0.8292 (ptm-80) cc_final: 0.7484 (ttp80) REVERT: H 161 MET cc_start: 0.7487 (ttp) cc_final: 0.6784 (tmt) REVERT: H 211 TYR cc_start: 0.7603 (m-80) cc_final: 0.5784 (t80) REVERT: H 257 GLU cc_start: 0.6048 (pt0) cc_final: 0.5788 (pp20) outliers start: 33 outliers final: 24 residues processed: 191 average time/residue: 3.0544 time to fit residues: 665.1158 Evaluate side-chains 186 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 213 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.1980 chunk 246 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 chunk 238 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS E 118 GLN F 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22107 Z= 0.225 Angle : 0.502 10.154 30104 Z= 0.266 Chirality : 0.039 0.146 3502 Planarity : 0.004 0.130 3653 Dihedral : 13.685 168.308 3363 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.39 % Allowed : 20.33 % Favored : 78.28 % 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: 1.36 (0.17), residues: 2584 helix: 1.89 (0.15), residues: 1210 sheet: 0.37 (0.22), residues: 518 loop : -0.08 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 638 HIS 0.005 0.001 HIS A 337 PHE 0.011 0.001 PHE E 328 TYR 0.017 0.001 TYR A 404 ARG 0.012 0.000 ARG E 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 3.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8702 (mp10) REVERT: A 732 MET cc_start: 0.8878 (mtt) cc_final: 0.8528 (mtt) REVERT: D 88 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8021 (ttp) REVERT: E 217 ASP cc_start: 0.7839 (t70) cc_final: 0.7610 (t0) REVERT: H 149 ARG cc_start: 0.8282 (ptm-80) cc_final: 0.7476 (ttp80) REVERT: H 161 MET cc_start: 0.7490 (ttp) cc_final: 0.6784 (tmt) REVERT: H 211 TYR cc_start: 0.7625 (m-80) cc_final: 0.5841 (t80) REVERT: H 257 GLU cc_start: 0.6083 (pt0) cc_final: 0.5772 (pp20) outliers start: 32 outliers final: 25 residues processed: 185 average time/residue: 3.1445 time to fit residues: 661.5156 Evaluate side-chains 188 residues out of total 2311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 213 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 190 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS E 118 GLN F 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.112759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.074096 restraints weight = 106883.188| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.65 r_work: 0.2895 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22107 Z= 0.246 Angle : 0.507 10.746 30104 Z= 0.269 Chirality : 0.040 0.146 3502 Planarity : 0.004 0.096 3653 Dihedral : 13.686 168.397 3363 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.34 % Allowed : 20.37 % Favored : 78.28 % 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: 1.35 (0.17), residues: 2584 helix: 1.86 (0.15), residues: 1212 sheet: 0.37 (0.22), residues: 516 loop : -0.07 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 638 HIS 0.004 0.001 HIS A 337 PHE 0.011 0.001 PHE E 328 TYR 0.015 0.001 TYR A 404 ARG 0.014 0.000 ARG G 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14109.75 seconds wall clock time: 246 minutes 57.43 seconds (14817.43 seconds total)