Starting phenix.real_space_refine on Tue Mar 19 20:56:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi5_33852/03_2024/7yi5_33852_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi5_33852/03_2024/7yi5_33852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi5_33852/03_2024/7yi5_33852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi5_33852/03_2024/7yi5_33852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi5_33852/03_2024/7yi5_33852_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi5_33852/03_2024/7yi5_33852_updated.pdb" } resolution = 3.96 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 302 5.49 5 S 87 5.16 5 C 15166 2.51 5 N 4501 2.21 5 O 5328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 811": "OE1" <-> "OE2" Residue "A GLU 822": "OE1" <-> "OE2" Residue "A GLU 911": "OE1" <-> "OE2" Residue "A PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "F ASP 550": "OD1" <-> "OD2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 41": "OE1" <-> "OE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "J TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "N TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "N GLU 73": "OE1" <-> "OE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 77": "OD1" <-> "OD2" Residue "K ASP 77": "OD1" <-> "OD2" Residue "K ASP 81": "OD1" <-> "OD2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25389 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4258 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 7, 'TRANS': 498} Chain breaks: 5 Chain: "B" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2923 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "C" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2326 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Chain: "D" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2626 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 302} Chain breaks: 5 Chain: "F" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 178 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "H" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "I" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "M" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "N" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "O" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3076 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "P" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3115 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 853 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9999 SG CYS D 263 106.230 97.946 71.560 1.00573.15 S ATOM 10016 SG CYS D 266 107.679 94.534 71.575 1.00560.27 S ATOM 10169 SG CYS D 286 109.562 97.207 73.325 1.00571.47 S ATOM 10080 SG CYS D 275 96.808 107.153 70.789 1.00661.37 S ATOM 10101 SG CYS D 278 98.603 107.038 67.692 1.00670.73 S ATOM 10327 SG CYS D 306 98.591 109.037 67.325 1.00705.46 S ATOM 11248 SG CYS D 440 128.858 65.635 63.691 1.00512.16 S ATOM 11274 SG CYS D 443 131.568 65.262 60.865 1.00521.23 S ATOM 11463 SG CYS D 466 132.509 64.378 64.355 1.00538.59 S ATOM 11060 SG CYS D 417 131.450 55.114 67.441 1.00536.70 S ATOM 11087 SG CYS D 420 131.195 51.337 67.907 1.00531.82 S ATOM 11343 SG CYS D 451 132.166 53.556 70.821 1.00493.39 S Time building chain proxies: 13.01, per 1000 atoms: 0.51 Number of scatterers: 25389 At special positions: 0 Unit cell: (186.19, 154.798, 137.477, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 87 16.00 P 302 15.00 O 5328 8.00 N 4501 7.00 C 15166 6.00 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: 14.27 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" ND1 HIS D 283 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 286 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 263 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 306 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 278 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 275 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 469 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 466 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 443 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 440 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" ND1 HIS D 448 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 417 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 451 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 420 " Number of angles added : 9 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4474 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 8 sheets defined 51.4% alpha, 4.9% beta 148 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 12.35 Creating SS restraints... Processing helix chain 'A' and resid 665 through 676 removed outlier: 4.068A pdb=" N PHE A 668 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N PHE A 669 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 676 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 699 through 710 Processing helix chain 'A' and resid 716 through 724 Processing helix chain 'A' and resid 760 through 763 Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 786 through 789 No H-bonds generated for 'chain 'A' and resid 786 through 789' Processing helix chain 'A' and resid 802 through 838 removed outlier: 3.754A pdb=" N LYS A 837 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 870 Processing helix chain 'A' and resid 876 through 884 removed outlier: 3.681A pdb=" N ASP A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 922 removed outlier: 4.331A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 927 No H-bonds generated for 'chain 'A' and resid 924 through 927' Processing helix chain 'A' and resid 930 through 934 removed outlier: 3.613A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 930 through 934' Processing helix chain 'A' and resid 938 through 942 Processing helix chain 'A' and resid 945 through 961 removed outlier: 3.872A pdb=" N ASN A 961 " --> pdb=" O VAL A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 998 Processing helix chain 'A' and resid 1004 through 1021 removed outlier: 3.961A pdb=" N GLU A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1030 No H-bonds generated for 'chain 'A' and resid 1028 through 1030' Processing helix chain 'A' and resid 1142 through 1163 Processing helix chain 'A' and resid 1165 through 1173 Processing helix chain 'A' and resid 1182 through 1185 No H-bonds generated for 'chain 'A' and resid 1182 through 1185' Processing helix chain 'A' and resid 1191 through 1194 No H-bonds generated for 'chain 'A' and resid 1191 through 1194' Processing helix chain 'A' and resid 1203 through 1216 Processing helix chain 'A' and resid 1221 through 1232 Processing helix chain 'A' and resid 1237 through 1239 No H-bonds generated for 'chain 'A' and resid 1237 through 1239' Processing helix chain 'A' and resid 1242 through 1257 Processing helix chain 'A' and resid 1260 through 1275 Processing helix chain 'A' and resid 1282 through 1292 Processing helix chain 'B' and resid 42 through 54 removed outlier: 4.031A pdb=" N ASN B 54 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.882A pdb=" N GLN B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 116 through 136 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 191 through 197 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 244 through 261 removed outlier: 3.774A pdb=" N SER B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 288 through 301 removed outlier: 3.966A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.872A pdb=" N ARG B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 347 Processing helix chain 'B' and resid 366 through 382 removed outlier: 4.701A pdb=" N ASN B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 72 No H-bonds generated for 'chain 'C' and resid 69 through 72' Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 102 through 123 Processing helix chain 'C' and resid 226 through 240 Processing helix chain 'C' and resid 254 through 266 Processing helix chain 'C' and resid 272 through 296 removed outlier: 4.984A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 316 removed outlier: 4.205A pdb=" N LEU C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 350 through 368 Processing helix chain 'C' and resid 392 through 400 Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 169 through 175 removed outlier: 3.855A pdb=" N GLU D 173 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET D 175 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 311 Processing helix chain 'D' and resid 317 through 327 Processing helix chain 'D' and resid 337 through 345 removed outlier: 4.165A pdb=" N ASP D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 406 Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 544 through 563 removed outlier: 3.910A pdb=" N ASP D 553 " --> pdb=" O ASP D 550 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL D 561 " --> pdb=" O SER D 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 562 Processing helix chain 'H' and resid 25 through 27 No H-bonds generated for 'chain 'H' and resid 25 through 27' Processing helix chain 'H' and resid 31 through 41 Processing helix chain 'H' and resid 50 through 75 removed outlier: 3.959A pdb=" N ASP H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 93 Processing helix chain 'I' and resid 17 through 21 Processing helix chain 'I' and resid 27 through 36 Processing helix chain 'I' and resid 45 through 73 removed outlier: 4.685A pdb=" N VAL I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 89 Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'J' and resid 35 through 45 Processing helix chain 'J' and resid 53 through 80 Processing helix chain 'J' and resid 88 through 98 Processing helix chain 'J' and resid 101 through 120 Processing helix chain 'L' and resid 26 through 28 No H-bonds generated for 'chain 'L' and resid 26 through 28' Processing helix chain 'L' and resid 31 through 40 Processing helix chain 'L' and resid 48 through 75 removed outlier: 4.060A pdb=" N TYR L 51 " --> pdb=" O GLY L 48 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU L 52 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG L 67 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 92 Processing helix chain 'M' and resid 17 through 21 Processing helix chain 'M' and resid 27 through 36 Processing helix chain 'M' and resid 47 through 72 Processing helix chain 'M' and resid 80 through 89 Processing helix chain 'M' and resid 91 through 96 Processing helix chain 'M' and resid 113 through 115 No H-bonds generated for 'chain 'M' and resid 113 through 115' Processing helix chain 'N' and resid 35 through 45 Processing helix chain 'N' and resid 53 through 81 Processing helix chain 'N' and resid 88 through 98 Processing helix chain 'N' and resid 101 through 120 Processing helix chain 'E' and resid 69 through 72 No H-bonds generated for 'chain 'E' and resid 69 through 72' Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 102 through 123 Processing helix chain 'G' and resid 45 through 54 Processing helix chain 'G' and resid 64 through 74 Processing helix chain 'G' and resid 86 through 113 Processing helix chain 'G' and resid 121 through 131 Processing helix chain 'K' and resid 45 through 54 Processing helix chain 'K' and resid 64 through 77 removed outlier: 4.081A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 113 Processing helix chain 'K' and resid 121 through 131 Processing sheet with id= A, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.039A pdb=" N HIS A1311 " --> pdb=" O ASP A1306 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A1306 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 61 through 64 removed outlier: 7.287A pdb=" N VAL B 21 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TYR B 64 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 23 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL B 141 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE B 24 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 143 " --> pdb=" O PHE B 24 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET B 305 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ASN B 144 " --> pdb=" O MET B 305 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL B 307 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 13 through 18 removed outlier: 6.479A pdb=" N PHE C 78 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 29 through 32 Processing sheet with id= E, first strand: chain 'D' and resid 364 through 366 Processing sheet with id= F, first strand: chain 'D' and resid 473 through 476 Processing sheet with id= G, first strand: chain 'E' and resid 13 through 18 removed outlier: 6.220A pdb=" N PHE E 78 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 29 through 32 860 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 377 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 148 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 14.29 Time building geometry restraints manager: 14.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7224 1.34 - 1.46: 7558 1.46 - 1.58: 10993 1.58 - 1.71: 602 1.71 - 1.83: 137 Bond restraints: 26514 Sorted by residual: bond pdb=" C LYS D 107 " pdb=" N VAL D 108 " ideal model delta sigma weight residual 1.332 1.351 -0.019 5.60e-03 3.19e+04 1.15e+01 bond pdb=" CA MET A 765 " pdb=" CB MET A 765 " ideal model delta sigma weight residual 1.526 1.552 -0.026 1.20e-02 6.94e+03 4.57e+00 bond pdb=" C SER K 86 " pdb=" N SER K 87 " ideal model delta sigma weight residual 1.335 1.315 0.020 1.32e-02 5.74e+03 2.37e+00 bond pdb=" C CYS D 451 " pdb=" N VAL D 452 " ideal model delta sigma weight residual 1.324 1.336 -0.012 8.60e-03 1.35e+04 1.96e+00 bond pdb=" SD MET B 47 " pdb=" CE MET B 47 " ideal model delta sigma weight residual 1.791 1.756 0.035 2.50e-02 1.60e+03 1.93e+00 ... (remaining 26509 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.16: 1260 104.16 - 111.66: 13192 111.66 - 119.15: 8705 119.15 - 126.65: 12839 126.65 - 134.15: 1066 Bond angle restraints: 37062 Sorted by residual: angle pdb=" C LEU N 98 " pdb=" N LEU N 99 " pdb=" CA LEU N 99 " ideal model delta sigma weight residual 122.15 107.25 14.90 3.47e+00 8.31e-02 1.84e+01 angle pdb=" N MET B 47 " pdb=" CA MET B 47 " pdb=" CB MET B 47 " ideal model delta sigma weight residual 110.39 117.13 -6.74 1.66e+00 3.63e-01 1.65e+01 angle pdb=" C ARG B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta sigma weight residual 120.72 114.20 6.52 1.67e+00 3.59e-01 1.52e+01 angle pdb=" C VAL K 89 " pdb=" N MET K 90 " pdb=" CA MET K 90 " ideal model delta sigma weight residual 121.14 114.50 6.64 1.75e+00 3.27e-01 1.44e+01 angle pdb=" CB MET C 37 " pdb=" CG MET C 37 " pdb=" SD MET C 37 " ideal model delta sigma weight residual 112.70 124.05 -11.35 3.00e+00 1.11e-01 1.43e+01 ... (remaining 37057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.96: 13099 30.96 - 61.92: 2002 61.92 - 92.88: 80 92.88 - 123.84: 0 123.84 - 154.80: 1 Dihedral angle restraints: 15182 sinusoidal: 8258 harmonic: 6924 Sorted by residual: dihedral pdb=" CA GLN D 541 " pdb=" C GLN D 541 " pdb=" N ILE D 542 " pdb=" CA ILE D 542 " ideal model delta harmonic sigma weight residual 180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PHE K 84 " pdb=" C PHE K 84 " pdb=" N GLN K 85 " pdb=" CA GLN K 85 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N LYS B 154 " pdb=" CA LYS B 154 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 15179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3443 0.053 - 0.107: 589 0.107 - 0.160: 46 0.160 - 0.213: 2 0.213 - 0.266: 2 Chirality restraints: 4082 Sorted by residual: chirality pdb=" CA MET K 90 " pdb=" N MET K 90 " pdb=" C MET K 90 " pdb=" CB MET K 90 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA MET B 47 " pdb=" N MET B 47 " pdb=" C MET B 47 " pdb=" CB MET B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL C 257 " pdb=" CA VAL C 257 " pdb=" CG1 VAL C 257 " pdb=" CG2 VAL C 257 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 4079 not shown) Planarity restraints: 3655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 296 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO D 297 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 297 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 297 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 118 " 0.043 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO D 119 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 57 " 0.040 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO E 58 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 58 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 58 " 0.033 5.00e-02 4.00e+02 ... (remaining 3652 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 333 2.58 - 3.16: 21912 3.16 - 3.74: 46835 3.74 - 4.32: 61531 4.32 - 4.90: 92165 Nonbonded interactions: 222776 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.006 2.230 nonbonded pdb=" OD2 ASP B 274 " pdb="ZN ZN B 501 " model vdw 2.016 2.230 nonbonded pdb=" O2 DC O 70 " pdb=" N2 DG P -70 " model vdw 2.054 2.496 nonbonded pdb=" OD1 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.058 2.230 nonbonded pdb=" O2 DC O -21 " pdb=" N2 DG P 21 " model vdw 2.083 2.496 ... (remaining 222771 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 'G' and (resid 36 through 109 or (resid 110 through 111 and (name N or na \ me CA or name C or name O or name CB )) or resid 112 through 134)) selection = chain 'K' } ncs_group { reference = chain 'H' selection = (chain 'L' and resid 23 through 101) } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.080 Check model and map are aligned: 0.430 Set scattering table: 0.230 Process input model: 89.260 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.005 0.047 26514 Z= 0.300 Angle : 0.665 14.903 37062 Z= 0.377 Chirality : 0.039 0.266 4082 Planarity : 0.004 0.067 3655 Dihedral : 23.555 154.797 10708 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.29 % Allowed : 20.67 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2307 helix: 1.52 (0.14), residues: 1265 sheet: -0.70 (0.50), residues: 128 loop : -1.57 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 464 HIS 0.010 0.002 HIS B 43 PHE 0.015 0.002 PHE B 301 TYR 0.015 0.001 TYR B 347 ARG 0.006 0.001 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 2.614 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: B 315 MET cc_start: 0.2566 (ptp) cc_final: 0.2311 (ptm) REVERT: E 22 MET cc_start: 0.4286 (mpp) cc_final: 0.4009 (mpp) outliers start: 6 outliers final: 1 residues processed: 74 average time/residue: 0.4071 time to fit residues: 49.0126 Evaluate side-chains 69 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 109 optimal weight: 30.0000 chunk 67 optimal weight: 50.0000 chunk 132 optimal weight: 30.0000 chunk 105 optimal weight: 30.0000 chunk 203 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 236 optimal weight: 0.0170 overall best weight: 7.2030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 GLN K 39 HIS K 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26514 Z= 0.298 Angle : 0.584 9.548 37062 Z= 0.334 Chirality : 0.038 0.185 4082 Planarity : 0.004 0.053 3655 Dihedral : 26.544 155.511 5896 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.25 % Allowed : 19.04 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2307 helix: 1.60 (0.14), residues: 1267 sheet: -0.74 (0.45), residues: 146 loop : -1.45 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 464 HIS 0.008 0.001 HIS L 75 PHE 0.016 0.001 PHE B 208 TYR 0.017 0.001 TYR C 38 ARG 0.004 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 65 time to evaluate : 2.662 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 1314 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8305 (mm) REVERT: B 128 MET cc_start: 0.7546 (tpp) cc_final: 0.7086 (tpp) outliers start: 47 outliers final: 15 residues processed: 105 average time/residue: 0.3843 time to fit residues: 64.6972 Evaluate side-chains 80 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain D residue 443 CYS Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 74 LYS Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 65 optimal weight: 30.0000 chunk 236 optimal weight: 50.0000 chunk 255 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 234 optimal weight: 40.0000 chunk 80 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26514 Z= 0.250 Angle : 0.555 9.449 37062 Z= 0.316 Chirality : 0.037 0.223 4082 Planarity : 0.004 0.048 3655 Dihedral : 26.522 155.053 5896 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.21 % Allowed : 19.47 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2307 helix: 1.70 (0.15), residues: 1264 sheet: -0.84 (0.45), residues: 136 loop : -1.34 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 464 HIS 0.005 0.001 HIS A 998 PHE 0.023 0.001 PHE A 685 TYR 0.013 0.001 TYR B 368 ARG 0.006 0.000 ARG A 906 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 64 time to evaluate : 2.876 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: A 1314 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8359 (mm) REVERT: B 128 MET cc_start: 0.7612 (tpp) cc_final: 0.7121 (tpp) REVERT: B 214 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8380 (t80) REVERT: D 438 MET cc_start: 0.8810 (pmm) cc_final: 0.8577 (pmm) REVERT: L 59 LYS cc_start: 0.9746 (pttt) cc_final: 0.9510 (ttpp) outliers start: 46 outliers final: 19 residues processed: 104 average time/residue: 0.4008 time to fit residues: 66.8682 Evaluate side-chains 85 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 64 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain M residue 74 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 50.0000 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 26 optimal weight: 50.0000 chunk 112 optimal weight: 30.0000 chunk 158 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 67 optimal weight: 40.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 ASN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 26514 Z= 0.314 Angle : 0.590 9.801 37062 Z= 0.335 Chirality : 0.038 0.190 4082 Planarity : 0.004 0.041 3655 Dihedral : 26.691 154.631 5896 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.02 % Allowed : 18.85 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2307 helix: 1.58 (0.14), residues: 1263 sheet: -0.94 (0.44), residues: 139 loop : -1.32 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 464 HIS 0.008 0.002 HIS A 998 PHE 0.018 0.002 PHE E 17 TYR 0.015 0.001 TYR C 38 ARG 0.005 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 63 time to evaluate : 2.877 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 668 PHE cc_start: 0.4461 (OUTLIER) cc_final: 0.3753 (t80) REVERT: B 128 MET cc_start: 0.7672 (tpp) cc_final: 0.7148 (tpp) REVERT: B 214 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8429 (t80) REVERT: E 22 MET cc_start: 0.2194 (OUTLIER) cc_final: 0.1943 (mpp) outliers start: 63 outliers final: 35 residues processed: 119 average time/residue: 0.3855 time to fit residues: 73.2310 Evaluate side-chains 101 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 63 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 74 LYS Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 0 optimal weight: 70.0000 chunk 128 optimal weight: 3.9990 chunk 225 optimal weight: 10.0000 chunk 63 optimal weight: 50.0000 overall best weight: 6.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN B 105 ASN ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26514 Z= 0.271 Angle : 0.575 10.020 37062 Z= 0.326 Chirality : 0.037 0.181 4082 Planarity : 0.004 0.040 3655 Dihedral : 26.730 155.050 5896 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.83 % Allowed : 19.86 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.17), residues: 2307 helix: 1.65 (0.15), residues: 1268 sheet: -1.06 (0.42), residues: 146 loop : -1.32 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 464 HIS 0.007 0.001 HIS A 998 PHE 0.015 0.001 PHE A1269 TYR 0.016 0.001 TYR B 347 ARG 0.004 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 64 time to evaluate : 2.712 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 668 PHE cc_start: 0.4632 (OUTLIER) cc_final: 0.3920 (t80) REVERT: B 128 MET cc_start: 0.7574 (tpp) cc_final: 0.7031 (tpp) REVERT: B 214 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8428 (t80) REVERT: C 253 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8412 (p) REVERT: D 438 MET cc_start: 0.8464 (pmm) cc_final: 0.8015 (pmm) REVERT: I 71 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8777 (ttp80) REVERT: N 68 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8763 (pt0) REVERT: G 120 MET cc_start: 0.8960 (ptp) cc_final: 0.8460 (mpp) outliers start: 59 outliers final: 40 residues processed: 116 average time/residue: 0.3997 time to fit residues: 74.0117 Evaluate side-chains 107 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 63 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 74 LYS Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 50.0000 chunk 226 optimal weight: 10.0000 chunk 49 optimal weight: 50.0000 chunk 147 optimal weight: 5.9990 chunk 62 optimal weight: 30.0000 chunk 251 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 83 optimal weight: 50.0000 chunk 132 optimal weight: 50.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 26514 Z= 0.355 Angle : 0.631 8.897 37062 Z= 0.356 Chirality : 0.039 0.185 4082 Planarity : 0.004 0.040 3655 Dihedral : 26.969 154.916 5896 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.31 % Allowed : 19.62 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2307 helix: 1.37 (0.14), residues: 1265 sheet: -1.15 (0.42), residues: 143 loop : -1.37 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 464 HIS 0.009 0.002 HIS A 998 PHE 0.016 0.002 PHE A1269 TYR 0.033 0.002 TYR B 232 ARG 0.006 0.001 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 59 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1165 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7745 (t0) REVERT: A 1298 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: B 128 MET cc_start: 0.7584 (tpp) cc_final: 0.6988 (tpp) REVERT: B 204 MET cc_start: -0.1001 (mmt) cc_final: -0.1947 (mmt) REVERT: B 214 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8352 (t80) REVERT: C 69 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8768 (tp30) REVERT: C 253 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8430 (p) REVERT: D 438 MET cc_start: 0.8077 (pmm) cc_final: 0.7187 (pmm) REVERT: I 71 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8795 (ttp80) outliers start: 69 outliers final: 42 residues processed: 122 average time/residue: 0.3921 time to fit residues: 76.3646 Evaluate side-chains 106 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 59 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 74 LYS Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 ASN M 73 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26514 Z= 0.193 Angle : 0.556 10.774 37062 Z= 0.314 Chirality : 0.036 0.213 4082 Planarity : 0.004 0.039 3655 Dihedral : 26.736 155.699 5896 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.06 % Allowed : 21.15 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2307 helix: 1.74 (0.15), residues: 1270 sheet: -1.02 (0.45), residues: 130 loop : -1.24 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 464 HIS 0.007 0.001 HIS A 998 PHE 0.012 0.001 PHE B 251 TYR 0.022 0.001 TYR B 232 ARG 0.004 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 62 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.7511 (tpp) cc_final: 0.6953 (tpp) REVERT: B 204 MET cc_start: -0.1146 (mmt) cc_final: -0.1980 (mmt) REVERT: B 214 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8381 (t80) REVERT: B 246 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6854 (p) REVERT: C 69 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8715 (tp30) REVERT: C 253 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8326 (p) REVERT: D 438 MET cc_start: 0.8123 (pmm) cc_final: 0.7265 (pmm) REVERT: I 59 THR cc_start: 0.9647 (OUTLIER) cc_final: 0.9427 (p) REVERT: N 68 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8731 (pt0) REVERT: G 120 MET cc_start: 0.8945 (ptp) cc_final: 0.8426 (mpp) outliers start: 43 outliers final: 32 residues processed: 101 average time/residue: 0.3872 time to fit residues: 62.5353 Evaluate side-chains 98 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 62 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain M residue 74 LYS Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 26514 Z= 0.195 Angle : 0.547 9.122 37062 Z= 0.309 Chirality : 0.036 0.191 4082 Planarity : 0.004 0.039 3655 Dihedral : 26.539 156.309 5896 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.16 % Allowed : 21.20 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2307 helix: 1.89 (0.15), residues: 1260 sheet: -0.95 (0.44), residues: 131 loop : -1.16 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 464 HIS 0.007 0.001 HIS A 998 PHE 0.012 0.001 PHE B 251 TYR 0.018 0.001 TYR B 232 ARG 0.003 0.000 ARG L 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 65 time to evaluate : 2.603 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: A 668 PHE cc_start: 0.5314 (OUTLIER) cc_final: 0.4585 (t80) REVERT: A 1164 MET cc_start: 0.9322 (mmp) cc_final: 0.8799 (tpt) REVERT: B 128 MET cc_start: 0.7534 (tpp) cc_final: 0.7007 (tpp) REVERT: B 204 MET cc_start: -0.1375 (mmt) cc_final: -0.2289 (mmt) REVERT: B 214 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8253 (t80) REVERT: B 246 THR cc_start: 0.7049 (OUTLIER) cc_final: 0.6775 (p) REVERT: C 69 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8785 (tp30) REVERT: C 253 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8270 (p) REVERT: D 438 MET cc_start: 0.8109 (pmm) cc_final: 0.7320 (pmm) REVERT: I 59 THR cc_start: 0.9653 (OUTLIER) cc_final: 0.9436 (p) REVERT: N 68 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8719 (pt0) outliers start: 45 outliers final: 37 residues processed: 106 average time/residue: 0.3938 time to fit residues: 67.4687 Evaluate side-chains 105 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 63 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 71 optimal weight: 30.0000 chunk 211 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 998 HIS A1299 ASN ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 26514 Z= 0.327 Angle : 0.620 9.382 37062 Z= 0.348 Chirality : 0.039 0.194 4082 Planarity : 0.004 0.042 3655 Dihedral : 26.929 156.800 5896 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.49 % Allowed : 20.91 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.17), residues: 2307 helix: 1.58 (0.15), residues: 1265 sheet: -1.01 (0.42), residues: 141 loop : -1.21 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 464 HIS 0.008 0.001 HIS A 998 PHE 0.013 0.002 PHE A1269 TYR 0.017 0.001 TYR B 347 ARG 0.005 0.001 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 61 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7771 (mpt180) REVERT: B 128 MET cc_start: 0.7571 (tpp) cc_final: 0.6985 (tpp) REVERT: B 204 MET cc_start: -0.1660 (mmt) cc_final: -0.2533 (mmt) REVERT: B 214 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8346 (t80) REVERT: B 246 THR cc_start: 0.7286 (OUTLIER) cc_final: 0.7020 (p) REVERT: C 69 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8656 (tp30) REVERT: C 253 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8343 (p) REVERT: D 438 MET cc_start: 0.7790 (pmm) cc_final: 0.7015 (pmm) REVERT: N 68 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8715 (pt0) REVERT: G 120 MET cc_start: 0.9107 (ptp) cc_final: 0.8645 (mpp) outliers start: 52 outliers final: 44 residues processed: 108 average time/residue: 0.4025 time to fit residues: 70.6841 Evaluate side-chains 109 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 61 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 4.9990 chunk 246 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 171 optimal weight: 5.9990 chunk 259 optimal weight: 8.9990 chunk 238 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26514 Z= 0.218 Angle : 0.572 11.365 37062 Z= 0.321 Chirality : 0.037 0.215 4082 Planarity : 0.004 0.045 3655 Dihedral : 26.757 156.760 5896 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.97 % Allowed : 21.39 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2307 helix: 1.66 (0.15), residues: 1279 sheet: -1.00 (0.43), residues: 141 loop : -1.12 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 464 HIS 0.005 0.001 HIS A 798 PHE 0.012 0.001 PHE A1198 TYR 0.016 0.001 TYR B 232 ARG 0.004 0.000 ARG C 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 61 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7711 (mpt180) REVERT: B 128 MET cc_start: 0.7506 (tpp) cc_final: 0.6953 (tpp) REVERT: B 204 MET cc_start: -0.1714 (mmt) cc_final: -0.2595 (mmt) REVERT: B 214 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8350 (t80) REVERT: B 246 THR cc_start: 0.7256 (OUTLIER) cc_final: 0.6992 (p) REVERT: C 22 MET cc_start: 0.6734 (mpp) cc_final: 0.5988 (mpp) REVERT: C 69 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8628 (tp30) REVERT: C 253 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8300 (p) REVERT: D 438 MET cc_start: 0.7931 (pmm) cc_final: 0.7255 (pmm) REVERT: N 68 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8718 (pt0) REVERT: E 110 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7899 (mmp80) REVERT: G 120 MET cc_start: 0.9026 (ptp) cc_final: 0.8533 (mpp) outliers start: 41 outliers final: 34 residues processed: 98 average time/residue: 0.3971 time to fit residues: 62.6228 Evaluate side-chains 100 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 61 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 30 optimal weight: 40.0000 chunk 57 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 38 optimal weight: 40.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.038149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.023774 restraints weight = 376049.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.024127 restraints weight = 204529.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.024422 restraints weight = 137943.277| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 26514 Z= 0.323 Angle : 0.629 11.117 37062 Z= 0.352 Chirality : 0.039 0.199 4082 Planarity : 0.004 0.044 3655 Dihedral : 26.951 156.778 5896 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.30 % Allowed : 20.96 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2307 helix: 1.50 (0.15), residues: 1260 sheet: -1.11 (0.42), residues: 141 loop : -1.12 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 464 HIS 0.011 0.002 HIS A1293 PHE 0.013 0.002 PHE A1269 TYR 0.016 0.001 TYR B 347 ARG 0.005 0.001 ARG C 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3497.35 seconds wall clock time: 65 minutes 54.48 seconds (3954.48 seconds total)