Starting phenix.real_space_refine on Sun Mar 17 05:39:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/03_2024/7xss_33433.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/03_2024/7xss_33433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/03_2024/7xss_33433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/03_2024/7xss_33433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/03_2024/7xss_33433.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xss_33433/03_2024/7xss_33433.pdb" } resolution = 3.2 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= 0.003 sd= 0.037 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 4 6.06 5 P 54 5.49 5 S 55 5.16 5 C 10509 2.51 5 N 2928 2.21 5 O 3297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C ASP 179": "OD1" <-> "OD2" Residue "C TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 490": "OD1" <-> "OD2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "C ASP 534": "OD1" <-> "OD2" Residue "C TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 563": "OD1" <-> "OD2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 674": "OE1" <-> "OE2" Residue "C GLU 690": "OE1" <-> "OE2" Residue "C TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 698": "OD1" <-> "OD2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 520": "OD1" <-> "OD2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 620": "OE1" <-> "OE2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 644": "OD1" <-> "OD2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 709": "OD1" <-> "OD2" Residue "B GLU 715": "OE1" <-> "OE2" Residue "B PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1002": "OE1" <-> "OE2" Residue "B PHE 1022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1471": "OD1" <-> "OD2" Residue "B GLU 1499": "OE1" <-> "OE2" Residue "B GLU 1504": "OE1" <-> "OE2" Residue "B PHE 1524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1565": "OD1" <-> "OD2" Residue "B PHE 1570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1600": "OE1" <-> "OE2" Residue "B ASP 1623": "OD1" <-> "OD2" Residue "B GLU 1650": "OE1" <-> "OE2" Residue "B GLU 1657": "OE1" <-> "OE2" Residue "B TYR 1663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1674": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16847 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 5361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5361 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 3 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 438 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 15} Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 14} Chain: "B" Number of atoms: 10336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1286, 10336 Unusual residues: {' ZN': 4} Classifications: {'peptide': 1282, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 60, 'TRANS': 1221, None: 4} Not linked: pdbres="GLN B1692 " pdbres=" ZN B1801 " Not linked: pdbres=" ZN B1801 " pdbres=" ZN B1802 " Not linked: pdbres=" ZN B1802 " pdbres=" ZN B1803 " Not linked: pdbres=" ZN B1803 " pdbres=" ZN B1804 " Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10251 SG CYS B 491 51.531 61.380 43.574 1.00 60.61 S ATOM 10319 SG CYS B 501 52.869 59.111 41.007 1.00 78.43 S ATOM 10333 SG CYS B 503 50.624 62.101 39.975 1.00 63.44 S ATOM 10355 SG CYS B 506 54.129 62.759 41.028 1.00 61.94 S ATOM 12320 SG CYS B 750 37.086 68.987 69.699 1.00 82.00 S ATOM 12333 SG CYS B 752 35.703 72.353 68.473 1.00 76.41 S ATOM 12355 SG CYS B 755 39.381 71.473 67.865 1.00 66.60 S ATOM 14333 SG CYS B1018 40.584 94.375 98.167 1.00 72.20 S ATOM 14504 SG CYS B1406 40.785 90.807 97.058 1.00 61.86 S ATOM 14555 SG CYS B1414 37.418 92.784 96.977 1.00 67.22 S ATOM 14572 SG CYS B1417 40.053 93.446 94.418 1.00 58.03 S ATOM 7187 SG CYS B 88 73.014 51.784 19.001 1.00 75.41 S ATOM 7458 SG CYS B 121 75.863 50.427 16.716 1.00 90.38 S ATOM 7504 SG CYS B 127 75.564 54.021 17.405 1.00 77.54 S ATOM 7528 SG CYS B 130 76.582 51.697 20.272 1.00 72.67 S Time building chain proxies: 9.02, per 1000 atoms: 0.54 Number of scatterers: 16847 At special positions: 0 Unit cell: (107.67, 152.29, 132.89, 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 4 29.99 S 55 16.00 P 54 15.00 O 3297 8.00 N 2928 7.00 C 10509 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: 6.29 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 491 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 503 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 501 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 506 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" ND1 HIS B 747 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 755 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 752 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1018 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1414 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1417 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1406 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 127 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 88 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 121 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 130 " Number of angles added : 21 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 39.4% alpha, 16.9% beta 5 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'C' and resid 21 through 33 removed outlier: 3.668A pdb=" N ASN C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 59 removed outlier: 4.053A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.625A pdb=" N PHE C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 110 removed outlier: 4.095A pdb=" N LYS C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 136 Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 163 through 177 removed outlier: 3.920A pdb=" N ILE C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 230 through 246 removed outlier: 4.330A pdb=" N ASP C 234 " --> pdb=" O HIS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 267 Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.674A pdb=" N GLN C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 320 removed outlier: 3.796A pdb=" N LYS C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 307 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 342 through 357 removed outlier: 3.543A pdb=" N LYS C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN C 357 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 448 Processing helix chain 'C' and resid 454 through 469 Processing helix chain 'C' and resid 470 through 474 removed outlier: 3.684A pdb=" N PHE C 473 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 3.551A pdb=" N GLY C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 500 " --> pdb=" O LEU C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 496 through 500' Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 566 through 572 removed outlier: 3.694A pdb=" N LEU C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.744A pdb=" N LEU C 611 " --> pdb=" O TYR C 607 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL C 614 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.766A pdb=" N GLY C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 677 removed outlier: 3.570A pdb=" N THR C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 677 " --> pdb=" O ILE C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 692 removed outlier: 4.472A pdb=" N TRP C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 692 " --> pdb=" O GLN C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.652A pdb=" N PHE C 703 " --> pdb=" O HIS C 699 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 59 through 78 removed outlier: 3.682A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 168 through 171 Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.528A pdb=" N ALA B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 287 removed outlier: 3.703A pdb=" N ASN B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.565A pdb=" N ILE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 354 through 375 Processing helix chain 'B' and resid 471 through 488 Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 617 through 624 Processing helix chain 'B' and resid 630 through 637 Processing helix chain 'B' and resid 688 through 692 Processing helix chain 'B' and resid 723 through 740 removed outlier: 3.523A pdb=" N HIS B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 744 Processing helix chain 'B' and resid 752 through 758 Processing helix chain 'B' and resid 776 through 780 removed outlier: 3.618A pdb=" N GLU B 779 " --> pdb=" O ASN B 776 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 780 " --> pdb=" O GLY B 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 776 through 780' Processing helix chain 'B' and resid 831 through 848 removed outlier: 3.840A pdb=" N GLY B 848 " --> pdb=" O ASP B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 859 removed outlier: 3.613A pdb=" N GLY B 859 " --> pdb=" O GLY B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 881 removed outlier: 3.790A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.724A pdb=" N ASP B 914 " --> pdb=" O SER B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1016 removed outlier: 3.901A pdb=" N LEU B1003 " --> pdb=" O PRO B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1394 through 1399 removed outlier: 3.595A pdb=" N LYS B1398 " --> pdb=" O THR B1394 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B1399 " --> pdb=" O LEU B1395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1394 through 1399' Processing helix chain 'B' and resid 1400 through 1404 Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1463 through 1468 removed outlier: 4.249A pdb=" N SER B1467 " --> pdb=" O ARG B1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 1486 through 1493 removed outlier: 3.972A pdb=" N ILE B1490 " --> pdb=" O GLY B1486 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B1493 " --> pdb=" O ILE B1489 " (cutoff:3.500A) Processing helix chain 'B' and resid 1493 through 1501 removed outlier: 4.147A pdb=" N GLU B1499 " --> pdb=" O LEU B1495 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B1501 " --> pdb=" O ILE B1497 " (cutoff:3.500A) Processing helix chain 'B' and resid 1528 through 1540 Processing helix chain 'B' and resid 1552 through 1556 Processing helix chain 'B' and resid 1583 through 1603 removed outlier: 3.558A pdb=" N GLY B1603 " --> pdb=" O ILE B1599 " (cutoff:3.500A) Processing helix chain 'B' and resid 1615 through 1618 removed outlier: 3.662A pdb=" N VAL B1618 " --> pdb=" O GLN B1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1615 through 1618' Processing helix chain 'B' and resid 1619 through 1629 Processing helix chain 'B' and resid 1673 through 1683 Processing sheet with id=AA1, first strand: chain 'C' and resid 425 through 431 Processing sheet with id=AA2, first strand: chain 'C' and resid 536 through 540 removed outlier: 6.355A pdb=" N LEU C 580 " --> pdb=" O ILE C 623 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLY C 625 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE C 582 " --> pdb=" O GLY C 625 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N CYS C 627 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR C 660 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C 626 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 173 through 181 removed outlier: 4.230A pdb=" N ASP B 190 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 13.679A pdb=" N ARG B 193 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N GLU B 22 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TRP B 195 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 11 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 238 " --> pdb=" O GLU B 11 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 109 through 111 removed outlier: 6.268A pdb=" N THR B 110 " --> pdb=" O VAL B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 512 through 514 removed outlier: 4.546A pdb=" N ARG B 421 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP B 606 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 423 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 604 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 514 removed outlier: 4.546A pdb=" N ARG B 421 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP B 606 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 423 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 604 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.690A pdb=" N VAL B 432 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN B 459 " --> pdb=" O VAL B 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.579A pdb=" N SER B 517 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 533 removed outlier: 10.509A pdb=" N GLU B 526 " --> pdb=" O ASP B 547 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASP B 547 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N ARG B 528 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N LEU B 545 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N ARG B 530 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N GLY B 543 " --> pdb=" O ARG B 530 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 532 " --> pdb=" O GLU B 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 703 through 704 removed outlier: 5.917A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 703 through 704 removed outlier: 5.917A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 865 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 787 through 792 removed outlier: 6.446A pdb=" N ALA B 803 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 920 through 921 Processing sheet with id=AB5, first strand: chain 'B' and resid 924 through 927 Processing sheet with id=AB6, first strand: chain 'B' and resid 991 through 992 removed outlier: 3.604A pdb=" N GLU B 995 " --> pdb=" O ILE B 992 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 991 through 992 removed outlier: 3.604A pdb=" N GLU B 995 " --> pdb=" O ILE B 992 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B1526 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU B 950 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER B 951 " --> pdb=" O THR B1569 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR B1569 " --> pdb=" O SER B 951 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS B 953 " --> pdb=" O LEU B1567 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B1567 " --> pdb=" O LYS B 953 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B 955 " --> pdb=" O ASP B1565 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 967 through 968 removed outlier: 4.449A pdb=" N LYS B 988 " --> pdb=" O ASP B 968 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE B 989 " --> pdb=" O GLU B1510 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1421 through 1422 626 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.62 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5262 1.34 - 1.46: 3315 1.46 - 1.58: 8572 1.58 - 1.70: 107 1.70 - 1.82: 76 Bond restraints: 17332 Sorted by residual: bond pdb=" CA ASN B 973 " pdb=" CB ASN B 973 " ideal model delta sigma weight residual 1.528 1.576 -0.048 1.67e-02 3.59e+03 8.20e+00 bond pdb=" CB PRO B 86 " pdb=" CG PRO B 86 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.27e+00 bond pdb=" N ASN B1544 " pdb=" CA ASN B1544 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 2.96e+00 bond pdb=" C ARG B1644 " pdb=" N TYR B1645 " ideal model delta sigma weight residual 1.333 1.374 -0.041 2.74e-02 1.33e+03 2.26e+00 bond pdb=" CB ASP B1565 " pdb=" CG ASP B1565 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.89e+00 ... (remaining 17327 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.01: 580 106.01 - 113.00: 9229 113.00 - 119.99: 6141 119.99 - 126.98: 7357 126.98 - 133.97: 320 Bond angle restraints: 23627 Sorted by residual: angle pdb=" CA PRO B 86 " pdb=" N PRO B 86 " pdb=" CD PRO B 86 " ideal model delta sigma weight residual 112.00 102.06 9.94 1.40e+00 5.10e-01 5.04e+01 angle pdb=" N VAL B 377 " pdb=" CA VAL B 377 " pdb=" C VAL B 377 " ideal model delta sigma weight residual 113.10 109.69 3.41 9.70e-01 1.06e+00 1.24e+01 angle pdb=" CA GLU B1496 " pdb=" CB GLU B1496 " pdb=" CG GLU B1496 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CA GLU C 268 " pdb=" CB GLU C 268 " pdb=" CG GLU C 268 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA ASP B1471 " pdb=" C ASP B1471 " pdb=" N GLU B1472 " ideal model delta sigma weight residual 116.84 122.20 -5.36 1.71e+00 3.42e-01 9.83e+00 ... (remaining 23622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 9980 35.92 - 71.83: 463 71.83 - 107.74: 34 107.74 - 143.66: 0 143.66 - 179.57: 4 Dihedral angle restraints: 10481 sinusoidal: 4888 harmonic: 5593 Sorted by residual: dihedral pdb=" O4' C D -7 " pdb=" C1' C D -7 " pdb=" N1 C D -7 " pdb=" C2 C D -7 " ideal model delta sinusoidal sigma weight residual 200.00 43.53 156.47 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' U D -8 " pdb=" C1' U D -8 " pdb=" N1 U D -8 " pdb=" C2 U D -8 " ideal model delta sinusoidal sigma weight residual -128.00 51.57 -179.57 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U D -14 " pdb=" C1' U D -14 " pdb=" N1 U D -14 " pdb=" C2 U D -14 " ideal model delta sinusoidal sigma weight residual -128.00 47.29 -175.29 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 10478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1936 0.040 - 0.079: 473 0.079 - 0.119: 136 0.119 - 0.158: 18 0.158 - 0.198: 3 Chirality restraints: 2566 Sorted by residual: chirality pdb=" CG LEU C 27 " pdb=" CB LEU C 27 " pdb=" CD1 LEU C 27 " pdb=" CD2 LEU C 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" C1' A D -16 " pdb=" O4' A D -16 " pdb=" C2' A D -16 " pdb=" N9 A D -16 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA ASN B1544 " pdb=" N ASN B1544 " pdb=" C ASN B1544 " pdb=" CB ASN B1544 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 2563 not shown) Planarity restraints: 2844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 85 " -0.097 5.00e-02 4.00e+02 1.38e-01 3.06e+01 pdb=" N PRO B 86 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 439 " -0.056 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO B 440 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 37 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO C 38 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 38 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 38 " 0.035 5.00e-02 4.00e+02 ... (remaining 2841 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 452 2.69 - 3.25: 15678 3.25 - 3.80: 25665 3.80 - 4.35: 33989 4.35 - 4.90: 56432 Nonbonded interactions: 132216 Sorted by model distance: nonbonded pdb=" O ALA C 626 " pdb=" OG1 THR C 660 " model vdw 2.143 2.440 nonbonded pdb=" NZ LYS B1571 " pdb=" OD1 ASN B1573 " model vdw 2.145 2.520 nonbonded pdb=" OP2 U D 6 " pdb=" OG SER B 854 " model vdw 2.148 2.440 nonbonded pdb=" OH TYR B1436 " pdb=" OE2 GLU B1441 " model vdw 2.160 2.440 nonbonded pdb=" OH TYR B 191 " pdb=" OD2 ASP B 386 " model vdw 2.174 2.440 ... (remaining 132211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 5.440 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 51.330 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.003 0.135 17332 Z= 0.196 Angle : 0.613 10.265 23627 Z= 0.346 Chirality : 0.039 0.198 2566 Planarity : 0.005 0.138 2844 Dihedral : 19.020 179.575 6887 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.72 % Favored : 94.18 % Rotamer: Outliers : 0.59 % Allowed : 27.57 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1924 helix: 1.43 (0.21), residues: 630 sheet: 0.88 (0.32), residues: 270 loop : -1.57 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 443 HIS 0.009 0.001 HIS B1621 PHE 0.019 0.001 PHE B1570 TYR 0.021 0.001 TYR C 696 ARG 0.009 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 365 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 164 GLU cc_start: 0.6278 (tm-30) cc_final: 0.6020 (tm-30) REVERT: C 250 LEU cc_start: 0.8337 (tt) cc_final: 0.8129 (tp) REVERT: C 518 TYR cc_start: 0.7400 (t80) cc_final: 0.7196 (t80) REVERT: C 630 ASP cc_start: 0.5532 (OUTLIER) cc_final: 0.5300 (m-30) REVERT: B 744 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7599 (mtpt) REVERT: B 836 LEU cc_start: 0.8269 (mp) cc_final: 0.7978 (mt) REVERT: B 973 ASN cc_start: 0.8289 (p0) cc_final: 0.8016 (p0) outliers start: 10 outliers final: 4 residues processed: 370 average time/residue: 0.3510 time to fit residues: 182.7613 Evaluate side-chains 349 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 344 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 348 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 ASN C 612 ASN B 112 GLN B 335 GLN B 615 ASN B 668 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17332 Z= 0.421 Angle : 0.654 7.975 23627 Z= 0.342 Chirality : 0.046 0.245 2566 Planarity : 0.006 0.090 2844 Dihedral : 15.370 177.585 2945 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.22 % Allowed : 23.93 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.19), residues: 1924 helix: 1.22 (0.20), residues: 639 sheet: 0.52 (0.33), residues: 255 loop : -1.58 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 612 HIS 0.007 0.002 HIS B 924 PHE 0.022 0.002 PHE B 156 TYR 0.022 0.002 TYR B 860 ARG 0.009 0.001 ARG B1491 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 401 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7203 (tm-30) REVERT: C 120 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7534 (mtp85) REVERT: C 134 ARG cc_start: 0.7790 (tmm-80) cc_final: 0.7370 (ttp80) REVERT: C 161 ASP cc_start: 0.7181 (m-30) cc_final: 0.6542 (t0) REVERT: C 164 GLU cc_start: 0.6477 (tm-30) cc_final: 0.6222 (tm-30) REVERT: C 216 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6487 (ptt) REVERT: C 218 LYS cc_start: 0.8025 (tptt) cc_final: 0.7751 (mtmm) REVERT: C 266 GLU cc_start: 0.7711 (tp30) cc_final: 0.7405 (tp30) REVERT: C 267 LYS cc_start: 0.8109 (mttp) cc_final: 0.7864 (mmmm) REVERT: C 318 ASP cc_start: 0.8431 (t0) cc_final: 0.8197 (t0) REVERT: C 400 TRP cc_start: 0.8220 (m100) cc_final: 0.8010 (m100) REVERT: C 508 LYS cc_start: 0.8382 (tppt) cc_final: 0.7941 (mmtm) REVERT: C 560 SER cc_start: 0.8196 (m) cc_final: 0.7840 (p) REVERT: C 650 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8485 (mp) REVERT: B 34 SER cc_start: 0.8582 (m) cc_final: 0.8246 (t) REVERT: B 171 ASP cc_start: 0.7687 (p0) cc_final: 0.7411 (t0) REVERT: B 178 LEU cc_start: 0.8913 (mt) cc_final: 0.8609 (mp) REVERT: B 313 LYS cc_start: 0.7866 (ptpp) cc_final: 0.7541 (mtmt) REVERT: B 349 SER cc_start: 0.8447 (p) cc_final: 0.8189 (m) REVERT: B 409 GLU cc_start: 0.7241 (mp0) cc_final: 0.7023 (pm20) REVERT: B 561 LEU cc_start: 0.8502 (tt) cc_final: 0.8220 (tp) REVERT: B 751 THR cc_start: 0.8774 (m) cc_final: 0.8540 (t) REVERT: B 849 LEU cc_start: 0.8632 (mt) cc_final: 0.8388 (mt) REVERT: B 973 ASN cc_start: 0.8308 (p0) cc_final: 0.8029 (p0) REVERT: B 997 MET cc_start: 0.8114 (ttp) cc_final: 0.7873 (ttm) REVERT: B 1496 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 1557 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7989 (t80) REVERT: B 1570 PHE cc_start: 0.8394 (p90) cc_final: 0.8163 (p90) outliers start: 89 outliers final: 51 residues processed: 451 average time/residue: 0.3414 time to fit residues: 217.9378 Evaluate side-chains 424 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 370 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 875 ASP Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1682 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 123 optimal weight: 0.0570 chunk 49 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 ASN C 576 ASN B 335 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17332 Z= 0.193 Angle : 0.535 6.026 23627 Z= 0.279 Chirality : 0.041 0.188 2566 Planarity : 0.005 0.070 2844 Dihedral : 15.286 178.147 2935 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.46 % Allowed : 24.40 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1924 helix: 1.51 (0.20), residues: 641 sheet: 0.49 (0.33), residues: 255 loop : -1.49 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 612 HIS 0.008 0.001 HIS B1621 PHE 0.017 0.001 PHE C 491 TYR 0.014 0.001 TYR B 860 ARG 0.005 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 377 time to evaluate : 1.811 Fit side-chains revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7324 (tm-30) REVERT: C 161 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6571 (t0) REVERT: C 164 GLU cc_start: 0.6352 (tm-30) cc_final: 0.6098 (tm-30) REVERT: C 216 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.6350 (ptt) REVERT: C 218 LYS cc_start: 0.8015 (tptt) cc_final: 0.7761 (mtmm) REVERT: C 266 GLU cc_start: 0.7680 (tp30) cc_final: 0.6971 (tp30) REVERT: C 267 LYS cc_start: 0.8013 (mttp) cc_final: 0.7754 (mmmm) REVERT: C 273 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7854 (mtt90) REVERT: C 508 LYS cc_start: 0.8308 (tppt) cc_final: 0.7938 (mmtm) REVERT: C 560 SER cc_start: 0.8159 (m) cc_final: 0.7833 (p) REVERT: C 585 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7596 (m90) REVERT: C 630 ASP cc_start: 0.5248 (OUTLIER) cc_final: 0.4937 (m-30) REVERT: C 641 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6775 (tm-30) REVERT: C 685 ASN cc_start: 0.7239 (t0) cc_final: 0.7012 (t0) REVERT: B 34 SER cc_start: 0.8509 (m) cc_final: 0.8206 (t) REVERT: B 171 ASP cc_start: 0.7613 (p0) cc_final: 0.7334 (t0) REVERT: B 178 LEU cc_start: 0.8902 (mt) cc_final: 0.8640 (mp) REVERT: B 313 LYS cc_start: 0.7866 (ptpp) cc_final: 0.7534 (mtmt) REVERT: B 349 SER cc_start: 0.8428 (p) cc_final: 0.8191 (m) REVERT: B 357 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7684 (mtpp) REVERT: B 361 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7172 (mpp) REVERT: B 384 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7995 (mt) REVERT: B 454 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7351 (mm-30) REVERT: B 591 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8334 (pp) REVERT: B 597 THR cc_start: 0.7932 (p) cc_final: 0.7173 (t) REVERT: B 617 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7731 (mmtt) REVERT: B 849 LEU cc_start: 0.8531 (mt) cc_final: 0.8260 (mt) REVERT: B 928 ASP cc_start: 0.6823 (p0) cc_final: 0.6553 (p0) REVERT: B 933 VAL cc_start: 0.8449 (t) cc_final: 0.8181 (m) REVERT: B 973 ASN cc_start: 0.8232 (p0) cc_final: 0.7940 (p0) REVERT: B 1496 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7182 (tm-30) REVERT: B 1557 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7945 (t80) REVERT: B 1691 PHE cc_start: 0.8063 (t80) cc_final: 0.7810 (t80) outliers start: 76 outliers final: 48 residues processed: 415 average time/residue: 0.3414 time to fit residues: 203.4671 Evaluate side-chains 423 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 366 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 121 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS C 553 ASN B 335 GLN ** B1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17332 Z= 0.181 Angle : 0.518 6.216 23627 Z= 0.269 Chirality : 0.040 0.195 2566 Planarity : 0.004 0.064 2844 Dihedral : 15.227 178.978 2935 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.22 % Allowed : 25.04 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1924 helix: 1.69 (0.20), residues: 641 sheet: 0.48 (0.33), residues: 255 loop : -1.43 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 PHE 0.019 0.001 PHE C 491 TYR 0.012 0.001 TYR B 578 ARG 0.005 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 386 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7380 (tm-30) REVERT: C 161 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6541 (t0) REVERT: C 164 GLU cc_start: 0.6327 (tm-30) cc_final: 0.6069 (tm-30) REVERT: C 266 GLU cc_start: 0.7694 (tp30) cc_final: 0.6954 (tp30) REVERT: C 267 LYS cc_start: 0.8002 (mttp) cc_final: 0.7754 (mmmm) REVERT: C 273 ARG cc_start: 0.8054 (mtt90) cc_final: 0.7791 (mtt90) REVERT: C 508 LYS cc_start: 0.8277 (tppt) cc_final: 0.7833 (mmtm) REVERT: C 547 PHE cc_start: 0.6840 (m-80) cc_final: 0.6537 (m-80) REVERT: C 560 SER cc_start: 0.8163 (m) cc_final: 0.7849 (p) REVERT: C 585 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7581 (m90) REVERT: C 641 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6744 (tm-30) REVERT: C 685 ASN cc_start: 0.7384 (t0) cc_final: 0.7175 (t0) REVERT: B 34 SER cc_start: 0.8495 (m) cc_final: 0.8200 (t) REVERT: B 171 ASP cc_start: 0.7597 (p0) cc_final: 0.7312 (p0) REVERT: B 178 LEU cc_start: 0.8911 (mt) cc_final: 0.8632 (mp) REVERT: B 313 LYS cc_start: 0.7859 (ptpp) cc_final: 0.7524 (mtmt) REVERT: B 345 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7034 (mt-10) REVERT: B 349 SER cc_start: 0.8435 (p) cc_final: 0.8196 (m) REVERT: B 357 LYS cc_start: 0.8158 (mtpp) cc_final: 0.7730 (mtpp) REVERT: B 361 MET cc_start: 0.7688 (tpp) cc_final: 0.7139 (mpp) REVERT: B 454 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7374 (mm-30) REVERT: B 591 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8304 (pp) REVERT: B 597 THR cc_start: 0.7888 (p) cc_final: 0.7129 (t) REVERT: B 751 THR cc_start: 0.8755 (m) cc_final: 0.8370 (t) REVERT: B 752 CYS cc_start: 0.7143 (p) cc_final: 0.6626 (p) REVERT: B 928 ASP cc_start: 0.6868 (p0) cc_final: 0.6666 (p0) REVERT: B 933 VAL cc_start: 0.8426 (t) cc_final: 0.8151 (m) REVERT: B 973 ASN cc_start: 0.8166 (p0) cc_final: 0.7852 (p0) REVERT: B 1443 LEU cc_start: 0.7873 (tp) cc_final: 0.7533 (tp) REVERT: B 1496 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7143 (tm-30) REVERT: B 1557 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7929 (t80) REVERT: B 1691 PHE cc_start: 0.8055 (t80) cc_final: 0.7806 (t80) outliers start: 72 outliers final: 51 residues processed: 420 average time/residue: 0.3603 time to fit residues: 217.3466 Evaluate side-chains 431 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 376 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 ASN B 498 GLN ** B1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17332 Z= 0.249 Angle : 0.552 9.744 23627 Z= 0.286 Chirality : 0.042 0.211 2566 Planarity : 0.005 0.061 2844 Dihedral : 15.266 178.856 2935 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.57 % Allowed : 24.11 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.19), residues: 1924 helix: 1.68 (0.20), residues: 641 sheet: 0.57 (0.33), residues: 247 loop : -1.45 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 612 HIS 0.008 0.001 HIS C 514 PHE 0.019 0.001 PHE C 491 TYR 0.016 0.001 TYR B 578 ARG 0.006 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 393 time to evaluate : 1.646 Fit side-chains revert: symmetry clash REVERT: C 30 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7186 (pp20) REVERT: C 102 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7384 (tm-30) REVERT: C 161 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6540 (t0) REVERT: C 164 GLU cc_start: 0.6392 (tm-30) cc_final: 0.6096 (tm-30) REVERT: C 218 LYS cc_start: 0.7928 (mtmm) cc_final: 0.7429 (mtmm) REVERT: C 266 GLU cc_start: 0.7683 (tp30) cc_final: 0.7014 (tp30) REVERT: C 267 LYS cc_start: 0.8132 (mttp) cc_final: 0.7826 (mmmm) REVERT: C 273 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7785 (mtt90) REVERT: C 483 ASP cc_start: 0.7746 (t70) cc_final: 0.7266 (t0) REVERT: C 508 LYS cc_start: 0.8155 (tppt) cc_final: 0.7774 (mmtm) REVERT: C 585 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7613 (m90) REVERT: C 685 ASN cc_start: 0.7507 (t0) cc_final: 0.7297 (t0) REVERT: B 142 VAL cc_start: 0.7827 (t) cc_final: 0.7544 (m) REVERT: B 171 ASP cc_start: 0.7643 (p0) cc_final: 0.7369 (p0) REVERT: B 178 LEU cc_start: 0.8905 (mt) cc_final: 0.8642 (mp) REVERT: B 313 LYS cc_start: 0.7900 (ptpp) cc_final: 0.7565 (mtmt) REVERT: B 349 SER cc_start: 0.8406 (p) cc_final: 0.8192 (m) REVERT: B 357 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7747 (mtpp) REVERT: B 361 MET cc_start: 0.7683 (tpp) cc_final: 0.7080 (mpp) REVERT: B 561 LEU cc_start: 0.8482 (tt) cc_final: 0.8231 (tp) REVERT: B 597 THR cc_start: 0.7992 (p) cc_final: 0.7228 (t) REVERT: B 752 CYS cc_start: 0.7086 (p) cc_final: 0.6572 (p) REVERT: B 933 VAL cc_start: 0.8420 (t) cc_final: 0.8160 (m) REVERT: B 973 ASN cc_start: 0.8126 (p0) cc_final: 0.7774 (p0) REVERT: B 1443 LEU cc_start: 0.7923 (tp) cc_final: 0.7719 (tp) REVERT: B 1496 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7102 (tm-30) REVERT: B 1557 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7950 (t80) REVERT: B 1593 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7896 (mtpp) REVERT: B 1691 PHE cc_start: 0.8061 (t80) cc_final: 0.7817 (t80) outliers start: 95 outliers final: 62 residues processed: 448 average time/residue: 0.3216 time to fit residues: 207.4124 Evaluate side-chains 451 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 386 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1422 THR Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1429 VAL Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 0.0060 chunk 47 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 HIS ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17332 Z= 0.211 Angle : 0.538 7.162 23627 Z= 0.279 Chirality : 0.041 0.216 2566 Planarity : 0.004 0.060 2844 Dihedral : 15.263 178.990 2935 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.10 % Allowed : 24.93 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1924 helix: 1.75 (0.20), residues: 641 sheet: 0.57 (0.34), residues: 244 loop : -1.44 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 612 HIS 0.012 0.001 HIS C 514 PHE 0.019 0.001 PHE C 491 TYR 0.018 0.001 TYR B 202 ARG 0.004 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 393 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7390 (tm-30) REVERT: C 161 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6507 (t0) REVERT: C 164 GLU cc_start: 0.6349 (tm-30) cc_final: 0.6066 (tm-30) REVERT: C 218 LYS cc_start: 0.7905 (mtmm) cc_final: 0.7351 (mtmm) REVERT: C 266 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6987 (tp30) REVERT: C 267 LYS cc_start: 0.8129 (mttp) cc_final: 0.7827 (mmmm) REVERT: C 273 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7785 (mtp85) REVERT: C 290 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8218 (tt) REVERT: C 354 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8416 (m) REVERT: C 483 ASP cc_start: 0.7803 (t70) cc_final: 0.7178 (t0) REVERT: C 508 LYS cc_start: 0.8147 (tppt) cc_final: 0.7824 (mmtm) REVERT: C 585 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7613 (m90) REVERT: C 685 ASN cc_start: 0.7503 (t0) cc_final: 0.7280 (t0) REVERT: C 688 GLN cc_start: 0.8269 (mt0) cc_final: 0.8044 (mt0) REVERT: B 142 VAL cc_start: 0.7823 (t) cc_final: 0.7543 (m) REVERT: B 171 ASP cc_start: 0.7635 (p0) cc_final: 0.7346 (p0) REVERT: B 178 LEU cc_start: 0.8874 (mt) cc_final: 0.8608 (mp) REVERT: B 313 LYS cc_start: 0.7894 (ptpp) cc_final: 0.7564 (mtmt) REVERT: B 357 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7722 (mtpp) REVERT: B 361 MET cc_start: 0.7678 (tpp) cc_final: 0.7013 (mpp) REVERT: B 561 LEU cc_start: 0.8475 (tt) cc_final: 0.8226 (tp) REVERT: B 597 THR cc_start: 0.7971 (p) cc_final: 0.7208 (t) REVERT: B 752 CYS cc_start: 0.7069 (p) cc_final: 0.6567 (p) REVERT: B 933 VAL cc_start: 0.8419 (t) cc_final: 0.8151 (m) REVERT: B 973 ASN cc_start: 0.8095 (p0) cc_final: 0.7750 (p0) REVERT: B 1443 LEU cc_start: 0.7926 (tp) cc_final: 0.7722 (tp) REVERT: B 1460 GLU cc_start: 0.7657 (tp30) cc_final: 0.7412 (tp30) REVERT: B 1496 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7081 (tm-30) REVERT: B 1557 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7933 (t80) REVERT: B 1593 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7895 (mtpp) REVERT: B 1691 PHE cc_start: 0.8017 (t80) cc_final: 0.7437 (t80) outliers start: 87 outliers final: 62 residues processed: 442 average time/residue: 0.3307 time to fit residues: 212.0633 Evaluate side-chains 450 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 382 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1422 THR Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1429 VAL Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 HIS C 514 HIS ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17332 Z= 0.185 Angle : 0.530 9.203 23627 Z= 0.275 Chirality : 0.040 0.212 2566 Planarity : 0.004 0.060 2844 Dihedral : 15.240 179.552 2935 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.69 % Allowed : 25.75 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 1924 helix: 1.92 (0.21), residues: 634 sheet: 0.57 (0.33), residues: 244 loop : -1.37 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 612 HIS 0.007 0.001 HIS C 514 PHE 0.020 0.001 PHE C 491 TYR 0.014 0.001 TYR B 578 ARG 0.004 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 388 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 ASP cc_start: 0.7007 (OUTLIER) cc_final: 0.6437 (t0) REVERT: C 164 GLU cc_start: 0.6326 (tm-30) cc_final: 0.6045 (tm-30) REVERT: C 187 LEU cc_start: 0.7843 (tp) cc_final: 0.7375 (tp) REVERT: C 218 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7412 (mtmm) REVERT: C 266 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6978 (tp30) REVERT: C 267 LYS cc_start: 0.8107 (mttp) cc_final: 0.7795 (mmmm) REVERT: C 483 ASP cc_start: 0.7730 (t70) cc_final: 0.7132 (t0) REVERT: C 508 LYS cc_start: 0.8160 (tppt) cc_final: 0.7821 (mmtm) REVERT: C 585 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.7575 (m90) REVERT: C 685 ASN cc_start: 0.7575 (t0) cc_final: 0.7274 (t0) REVERT: C 688 GLN cc_start: 0.8225 (mt0) cc_final: 0.7825 (mt0) REVERT: B 142 VAL cc_start: 0.7815 (t) cc_final: 0.7525 (m) REVERT: B 171 ASP cc_start: 0.7578 (p0) cc_final: 0.7257 (p0) REVERT: B 178 LEU cc_start: 0.8852 (mt) cc_final: 0.8594 (mp) REVERT: B 218 LYS cc_start: 0.8525 (tppt) cc_final: 0.8275 (mmtm) REVERT: B 313 LYS cc_start: 0.7916 (ptpp) cc_final: 0.7580 (mtmt) REVERT: B 357 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7695 (mtpp) REVERT: B 361 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7017 (mpp) REVERT: B 384 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7979 (mt) REVERT: B 561 LEU cc_start: 0.8484 (tt) cc_final: 0.8243 (tp) REVERT: B 597 THR cc_start: 0.7941 (p) cc_final: 0.7178 (t) REVERT: B 752 CYS cc_start: 0.7042 (p) cc_final: 0.6531 (p) REVERT: B 933 VAL cc_start: 0.8405 (t) cc_final: 0.8153 (m) REVERT: B 973 ASN cc_start: 0.8049 (p0) cc_final: 0.7703 (p0) REVERT: B 997 MET cc_start: 0.8029 (ttm) cc_final: 0.7815 (mtm) REVERT: B 1496 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7076 (tm-30) REVERT: B 1557 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7887 (t80) REVERT: B 1593 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7892 (mtpp) REVERT: B 1691 PHE cc_start: 0.8061 (t80) cc_final: 0.7216 (t80) outliers start: 80 outliers final: 59 residues processed: 427 average time/residue: 0.3383 time to fit residues: 207.3583 Evaluate side-chains 445 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 380 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1422 THR Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 130 optimal weight: 0.0370 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 174 optimal weight: 0.0030 overall best weight: 0.5470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17332 Z= 0.177 Angle : 0.529 10.281 23627 Z= 0.275 Chirality : 0.040 0.236 2566 Planarity : 0.004 0.061 2844 Dihedral : 15.235 179.752 2935 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.52 % Allowed : 25.75 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1924 helix: 1.98 (0.21), residues: 633 sheet: 0.62 (0.33), residues: 244 loop : -1.35 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 400 HIS 0.006 0.001 HIS B1621 PHE 0.024 0.001 PHE B1691 TYR 0.019 0.001 TYR B 202 ARG 0.004 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 385 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6466 (t0) REVERT: C 164 GLU cc_start: 0.6314 (tm-30) cc_final: 0.6036 (tm-30) REVERT: C 187 LEU cc_start: 0.7833 (tp) cc_final: 0.7377 (tp) REVERT: C 218 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7390 (mtmm) REVERT: C 266 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: C 267 LYS cc_start: 0.8093 (mttp) cc_final: 0.7785 (mmmm) REVERT: C 483 ASP cc_start: 0.7729 (t70) cc_final: 0.7085 (t0) REVERT: C 508 LYS cc_start: 0.8163 (tppt) cc_final: 0.7830 (mmtm) REVERT: C 534 ASP cc_start: 0.7636 (p0) cc_final: 0.7358 (p0) REVERT: C 556 TRP cc_start: 0.5498 (OUTLIER) cc_final: 0.3289 (p90) REVERT: C 585 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.7545 (m90) REVERT: C 685 ASN cc_start: 0.7570 (t0) cc_final: 0.7287 (t0) REVERT: C 688 GLN cc_start: 0.8215 (mt0) cc_final: 0.7832 (mt0) REVERT: B 142 VAL cc_start: 0.7808 (t) cc_final: 0.7521 (m) REVERT: B 171 ASP cc_start: 0.7584 (p0) cc_final: 0.7246 (p0) REVERT: B 178 LEU cc_start: 0.8853 (mt) cc_final: 0.8579 (mp) REVERT: B 218 LYS cc_start: 0.8524 (tppt) cc_final: 0.8267 (mmtm) REVERT: B 313 LYS cc_start: 0.7891 (ptpp) cc_final: 0.7566 (mtmt) REVERT: B 357 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7672 (mtpp) REVERT: B 361 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7016 (mpp) REVERT: B 384 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7996 (mt) REVERT: B 561 LEU cc_start: 0.8464 (tt) cc_final: 0.8227 (tp) REVERT: B 597 THR cc_start: 0.7933 (p) cc_final: 0.7166 (t) REVERT: B 633 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7147 (tp30) REVERT: B 717 GLU cc_start: 0.7074 (pm20) cc_final: 0.6826 (pm20) REVERT: B 752 CYS cc_start: 0.7029 (p) cc_final: 0.6518 (p) REVERT: B 933 VAL cc_start: 0.8426 (t) cc_final: 0.8160 (m) REVERT: B 973 ASN cc_start: 0.8038 (p0) cc_final: 0.7690 (p0) REVERT: B 997 MET cc_start: 0.7994 (ttm) cc_final: 0.7763 (mtm) REVERT: B 1496 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7065 (tm-30) REVERT: B 1557 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7938 (t80) REVERT: B 1593 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7896 (mtpp) outliers start: 77 outliers final: 60 residues processed: 424 average time/residue: 0.3246 time to fit residues: 196.9977 Evaluate side-chains 449 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 381 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 556 TRP Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1422 THR Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 161 optimal weight: 0.0670 chunk 169 optimal weight: 6.9990 chunk 117 optimal weight: 0.2980 chunk 189 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 HIS C 514 HIS ** B1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17332 Z= 0.173 Angle : 0.526 10.236 23627 Z= 0.273 Chirality : 0.040 0.239 2566 Planarity : 0.004 0.062 2844 Dihedral : 15.233 179.977 2935 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.40 % Allowed : 26.16 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 1924 helix: 2.03 (0.21), residues: 633 sheet: 0.71 (0.33), residues: 243 loop : -1.35 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 400 HIS 0.007 0.001 HIS C 514 PHE 0.020 0.001 PHE B1691 TYR 0.013 0.001 TYR B 578 ARG 0.003 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 385 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6462 (t0) REVERT: C 164 GLU cc_start: 0.6317 (tm-30) cc_final: 0.6033 (tm-30) REVERT: C 187 LEU cc_start: 0.7809 (tp) cc_final: 0.7439 (tp) REVERT: C 218 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7294 (mtmm) REVERT: C 266 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6930 (tp30) REVERT: C 267 LYS cc_start: 0.8090 (mttp) cc_final: 0.7777 (mmmm) REVERT: C 508 LYS cc_start: 0.8193 (tppt) cc_final: 0.7845 (mmtm) REVERT: C 556 TRP cc_start: 0.5541 (OUTLIER) cc_final: 0.3353 (p90) REVERT: C 585 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7527 (m90) REVERT: C 685 ASN cc_start: 0.7600 (t0) cc_final: 0.7288 (t0) REVERT: C 688 GLN cc_start: 0.8208 (mt0) cc_final: 0.7813 (mt0) REVERT: B 36 MET cc_start: 0.8590 (mmm) cc_final: 0.8386 (tpt) REVERT: B 142 VAL cc_start: 0.7797 (t) cc_final: 0.7503 (m) REVERT: B 171 ASP cc_start: 0.7579 (p0) cc_final: 0.7251 (p0) REVERT: B 178 LEU cc_start: 0.8840 (mt) cc_final: 0.8582 (mp) REVERT: B 218 LYS cc_start: 0.8522 (tppt) cc_final: 0.8265 (mmtm) REVERT: B 313 LYS cc_start: 0.7891 (ptpp) cc_final: 0.7571 (mtmt) REVERT: B 357 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7668 (mtpp) REVERT: B 361 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7019 (mpp) REVERT: B 384 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7991 (mt) REVERT: B 561 LEU cc_start: 0.8459 (tt) cc_final: 0.8221 (tp) REVERT: B 597 THR cc_start: 0.7908 (p) cc_final: 0.7144 (t) REVERT: B 717 GLU cc_start: 0.7082 (pm20) cc_final: 0.6760 (pm20) REVERT: B 752 CYS cc_start: 0.7025 (p) cc_final: 0.6510 (p) REVERT: B 933 VAL cc_start: 0.8425 (t) cc_final: 0.8160 (m) REVERT: B 973 ASN cc_start: 0.8042 (p0) cc_final: 0.7693 (p0) REVERT: B 997 MET cc_start: 0.7976 (ttm) cc_final: 0.7753 (mtm) REVERT: B 1496 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7061 (tm-30) REVERT: B 1523 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7920 (mtp-110) REVERT: B 1557 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7939 (t80) REVERT: B 1593 LYS cc_start: 0.8224 (mtpp) cc_final: 0.7896 (mtpp) outliers start: 75 outliers final: 60 residues processed: 424 average time/residue: 0.3358 time to fit residues: 203.9768 Evaluate side-chains 447 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 380 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 TRP Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 615 LYS Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1422 THR Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 198 optimal weight: 0.4980 chunk 182 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 HIS C 514 HIS B1649 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17332 Z= 0.222 Angle : 0.551 10.578 23627 Z= 0.285 Chirality : 0.041 0.238 2566 Planarity : 0.004 0.062 2844 Dihedral : 15.263 179.569 2935 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.11 % Allowed : 26.39 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 1924 helix: 1.92 (0.21), residues: 640 sheet: 0.64 (0.33), residues: 245 loop : -1.37 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 400 HIS 0.008 0.001 HIS C 514 PHE 0.018 0.001 PHE C 491 TYR 0.014 0.001 TYR B 578 ARG 0.003 0.000 ARG C 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 389 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 29 ASP cc_start: 0.7254 (t0) cc_final: 0.6752 (m-30) REVERT: C 161 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6434 (t0) REVERT: C 164 GLU cc_start: 0.6381 (tm-30) cc_final: 0.6089 (tm-30) REVERT: C 187 LEU cc_start: 0.7799 (tp) cc_final: 0.7419 (tp) REVERT: C 218 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7284 (mtmm) REVERT: C 266 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6926 (tp30) REVERT: C 267 LYS cc_start: 0.8158 (mttp) cc_final: 0.7836 (mmmm) REVERT: C 508 LYS cc_start: 0.8175 (tppt) cc_final: 0.7849 (mmtm) REVERT: C 556 TRP cc_start: 0.5714 (OUTLIER) cc_final: 0.3069 (p90) REVERT: C 585 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7589 (m90) REVERT: C 685 ASN cc_start: 0.7660 (t0) cc_final: 0.7347 (t0) REVERT: C 688 GLN cc_start: 0.8225 (mt0) cc_final: 0.7822 (mt0) REVERT: B 142 VAL cc_start: 0.7843 (t) cc_final: 0.7550 (m) REVERT: B 171 ASP cc_start: 0.7573 (p0) cc_final: 0.7268 (p0) REVERT: B 178 LEU cc_start: 0.8864 (mt) cc_final: 0.8606 (mp) REVERT: B 218 LYS cc_start: 0.8528 (tppt) cc_final: 0.8276 (mmtm) REVERT: B 313 LYS cc_start: 0.7870 (ptpp) cc_final: 0.7546 (mtmt) REVERT: B 357 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7698 (mtpp) REVERT: B 361 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7007 (mpp) REVERT: B 561 LEU cc_start: 0.8451 (tt) cc_final: 0.8213 (tp) REVERT: B 597 THR cc_start: 0.7961 (p) cc_final: 0.7199 (t) REVERT: B 717 GLU cc_start: 0.7142 (pm20) cc_final: 0.6680 (pm20) REVERT: B 752 CYS cc_start: 0.7020 (p) cc_final: 0.6499 (p) REVERT: B 933 VAL cc_start: 0.8423 (t) cc_final: 0.8161 (m) REVERT: B 973 ASN cc_start: 0.8028 (p0) cc_final: 0.7660 (p0) REVERT: B 997 MET cc_start: 0.8049 (ttm) cc_final: 0.7815 (mtm) REVERT: B 1496 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7066 (tm-30) REVERT: B 1523 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7938 (mtp-110) REVERT: B 1557 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.7980 (t80) REVERT: B 1593 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7906 (mtpp) outliers start: 70 outliers final: 56 residues processed: 427 average time/residue: 0.3283 time to fit residues: 202.3333 Evaluate side-chains 450 residues out of total 1707 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 388 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 556 TRP Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1422 THR Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 158 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 HIS C 514 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108703 restraints weight = 24184.826| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.07 r_work: 0.3217 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17332 Z= 0.191 Angle : 0.538 10.761 23627 Z= 0.279 Chirality : 0.040 0.236 2566 Planarity : 0.004 0.063 2844 Dihedral : 15.247 179.692 2935 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.93 % Allowed : 26.69 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 1924 helix: 2.02 (0.21), residues: 633 sheet: 0.62 (0.33), residues: 245 loop : -1.34 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 400 HIS 0.008 0.001 HIS C 514 PHE 0.019 0.001 PHE C 491 TYR 0.020 0.001 TYR B 202 ARG 0.003 0.000 ARG C 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4640.83 seconds wall clock time: 83 minutes 26.78 seconds (5006.78 seconds total)