Starting phenix.real_space_refine on Sun Feb 18 11:08:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfu_22856/02_2024/7kfu_22856.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfu_22856/02_2024/7kfu_22856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfu_22856/02_2024/7kfu_22856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfu_22856/02_2024/7kfu_22856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfu_22856/02_2024/7kfu_22856.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfu_22856/02_2024/7kfu_22856.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 13912 2.51 5 N 3988 2.21 5 O 3902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 455": "OE1" <-> "OE2" Residue "C ASP 456": "OD1" <-> "OD2" Residue "C PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 463": "NH1" <-> "NH2" Residue "C ASP 477": "OD1" <-> "OD2" Residue "C ASP 495": "OD1" <-> "OD2" Residue "C ASP 523": "OD1" <-> "OD2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "C PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 541": "OD1" <-> "OD2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ASP 666": "OD1" <-> "OD2" Residue "C ASP 675": "OD1" <-> "OD2" Residue "C GLU 685": "OE1" <-> "OE2" Residue "C TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 774": "NH1" <-> "NH2" Residue "C ARG 801": "NH1" <-> "NH2" Residue "C ARG 834": "NH1" <-> "NH2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "C PHE 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 891": "NH1" <-> "NH2" Residue "C ASP 911": "OD1" <-> "OD2" Residue "C ARG 913": "NH1" <-> "NH2" Residue "C ASP 917": "OD1" <-> "OD2" Residue "C ARG 932": "NH1" <-> "NH2" Residue "C PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 659": "OD1" <-> "OD2" Residue "D ASP 666": "OD1" <-> "OD2" Residue "D GLU 708": "OE1" <-> "OE2" Residue "D TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 748": "NH1" <-> "NH2" Residue "D PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 763": "NH1" <-> "NH2" Residue "D GLU 808": "OE1" <-> "OE2" Residue "D GLU 814": "OE1" <-> "OE2" Residue "D ARG 834": "NH1" <-> "NH2" Residue "D ARG 835": "NH1" <-> "NH2" Residue "D ASP 857": "OD1" <-> "OD2" Residue "D ASP 885": "OD1" <-> "OD2" Residue "D GLU 888": "OE1" <-> "OE2" Residue "D TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 913": "NH1" <-> "NH2" Residue "D ASP 917": "OD1" <-> "OD2" Residue "D ASP 922": "OD1" <-> "OD2" Residue "D ARG 931": "NH1" <-> "NH2" Residue "D TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 199": "NH1" <-> "NH2" Residue "E TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 292": "NH1" <-> "NH2" Residue "E TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 322": "NH1" <-> "NH2" Residue "E ASP 350": "OD1" <-> "OD2" Residue "E TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 455": "OE1" <-> "OE2" Residue "E ASP 456": "OD1" <-> "OD2" Residue "E PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 463": "NH1" <-> "NH2" Residue "E ASP 477": "OD1" <-> "OD2" Residue "E ASP 495": "OD1" <-> "OD2" Residue "E ASP 523": "OD1" <-> "OD2" Residue "E GLU 529": "OE1" <-> "OE2" Residue "E PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 541": "OD1" <-> "OD2" Residue "E GLU 565": "OE1" <-> "OE2" Residue "E PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 592": "NH1" <-> "NH2" Residue "E ASP 666": "OD1" <-> "OD2" Residue "E ASP 675": "OD1" <-> "OD2" Residue "E GLU 685": "OE1" <-> "OE2" Residue "E TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 774": "NH1" <-> "NH2" Residue "E ARG 801": "NH1" <-> "NH2" Residue "E ARG 834": "NH1" <-> "NH2" Residue "E ASP 839": "OD1" <-> "OD2" Residue "E PHE 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 891": "NH1" <-> "NH2" Residue "E ASP 911": "OD1" <-> "OD2" Residue "E ARG 913": "NH1" <-> "NH2" Residue "E ASP 917": "OD1" <-> "OD2" Residue "E ARG 932": "NH1" <-> "NH2" Residue "E PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 659": "OD1" <-> "OD2" Residue "F ASP 666": "OD1" <-> "OD2" Residue "F GLU 708": "OE1" <-> "OE2" Residue "F TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 748": "NH1" <-> "NH2" Residue "F PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 763": "NH1" <-> "NH2" Residue "F GLU 808": "OE1" <-> "OE2" Residue "F GLU 814": "OE1" <-> "OE2" Residue "F ARG 834": "NH1" <-> "NH2" Residue "F ARG 835": "NH1" <-> "NH2" Residue "F ASP 857": "OD1" <-> "OD2" Residue "F ASP 885": "OD1" <-> "OD2" Residue "F GLU 888": "OE1" <-> "OE2" Residue "F TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 913": "NH1" <-> "NH2" Residue "F ASP 917": "OD1" <-> "OD2" Residue "F ASP 922": "OD1" <-> "OD2" Residue "F ARG 931": "NH1" <-> "NH2" Residue "F TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21848 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "C" Number of atoms: 7401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 7401 Classifications: {'peptide': 909} Link IDs: {'PTRANS': 33, 'TRANS': 875} Chain breaks: 6 Chain: "D" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2727 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "E" Number of atoms: 7401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 7401 Classifications: {'peptide': 909} Link IDs: {'PTRANS': 33, 'TRANS': 875} Chain breaks: 6 Chain: "F" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2727 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Time building chain proxies: 10.85, per 1000 atoms: 0.50 Number of scatterers: 21848 At special positions: 0 Unit cell: (148.375, 142.44, 179.237, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 3902 8.00 N 3988 7.00 C 13912 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: 8.37 Conformation dependent library (CDL) restraints added in 4.0 seconds 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5092 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 20 sheets defined 49.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.832A pdb=" N LYS A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 60 removed outlier: 3.953A pdb=" N LYS A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 24 removed outlier: 3.699A pdb=" N GLU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 57 removed outlier: 3.661A pdb=" N LYS B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 72 through 79 removed outlier: 3.510A pdb=" N ILE B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 41 Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 80 through 91 removed outlier: 4.263A pdb=" N HIS C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 150 removed outlier: 4.004A pdb=" N TRP C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.718A pdb=" N TYR C 184 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 211 removed outlier: 3.883A pdb=" N PHE C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.510A pdb=" N LEU C 227 " --> pdb=" O HIS C 223 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.949A pdb=" N LEU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET C 286 " --> pdb=" O ILE C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.542A pdb=" N CYS C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 352 through 370 removed outlier: 3.782A pdb=" N THR C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 420 Proline residue: C 412 - end of helix Processing helix chain 'C' and resid 430 through 445 Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.646A pdb=" N ASP C 456 " --> pdb=" O ASP C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 474 removed outlier: 3.798A pdb=" N LEU C 466 " --> pdb=" O TYR C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 488 removed outlier: 4.218A pdb=" N GLN C 482 " --> pdb=" O PRO C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 518 removed outlier: 4.371A pdb=" N LEU C 515 " --> pdb=" O PRO C 511 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN C 518 " --> pdb=" O PRO C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 523 removed outlier: 3.546A pdb=" N ASP C 523 " --> pdb=" O ILE C 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 523' Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'C' and resid 549 through 572 removed outlier: 3.896A pdb=" N GLN C 553 " --> pdb=" O GLN C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 587 Processing helix chain 'C' and resid 620 through 628 removed outlier: 4.118A pdb=" N ALA C 624 " --> pdb=" O PRO C 620 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN C 625 " --> pdb=" O PRO C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 709 Processing helix chain 'C' and resid 736 through 746 Processing helix chain 'C' and resid 748 through 771 Processing helix chain 'C' and resid 772 through 773 No H-bonds generated for 'chain 'C' and resid 772 through 773' Processing helix chain 'C' and resid 774 through 780 removed outlier: 3.538A pdb=" N HIS C 777 " --> pdb=" O ARG C 774 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LYS C 779 " --> pdb=" O ALA C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 796 removed outlier: 3.636A pdb=" N LEU C 785 " --> pdb=" O LEU C 781 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 796 " --> pdb=" O GLN C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 817 removed outlier: 4.508A pdb=" N ASN C 805 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY C 806 " --> pdb=" O SER C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 828 removed outlier: 3.737A pdb=" N HIS C 828 " --> pdb=" O GLU C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 864 removed outlier: 3.700A pdb=" N VAL C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU C 844 " --> pdb=" O PRO C 840 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 845 " --> pdb=" O PHE C 841 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR C 850 " --> pdb=" O SER C 846 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 887 Processing helix chain 'C' and resid 896 through 904 Processing helix chain 'C' and resid 927 through 944 Processing helix chain 'C' and resid 951 through 968 removed outlier: 4.033A pdb=" N GLN C 957 " --> pdb=" O GLN C 953 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 709 Processing helix chain 'D' and resid 728 through 733 Processing helix chain 'D' and resid 739 through 746 Processing helix chain 'D' and resid 748 through 773 removed outlier: 3.710A pdb=" N VAL D 760 " --> pdb=" O ALA D 756 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU D 771 " --> pdb=" O GLN D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 794 removed outlier: 5.026A pdb=" N GLN D 783 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR D 784 " --> pdb=" O GLN D 780 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 794 " --> pdb=" O LYS D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 817 removed outlier: 3.525A pdb=" N LEU D 804 " --> pdb=" O LYS D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 822 Processing helix chain 'D' and resid 839 through 863 removed outlier: 3.741A pdb=" N VAL D 843 " --> pdb=" O ASP D 839 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 863 " --> pdb=" O ILE D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 887 Processing helix chain 'D' and resid 891 through 904 removed outlier: 3.816A pdb=" N GLU D 895 " --> pdb=" O ARG D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 910 No H-bonds generated for 'chain 'D' and resid 908 through 910' Processing helix chain 'D' and resid 927 through 944 Processing helix chain 'D' and resid 950 through 969 Processing helix chain 'E' and resid 28 through 41 Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 80 through 91 removed outlier: 4.263A pdb=" N HIS E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 150 removed outlier: 4.003A pdb=" N TRP E 147 " --> pdb=" O GLN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 180 through 184 removed outlier: 3.718A pdb=" N TYR E 184 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 211 removed outlier: 3.883A pdb=" N PHE E 211 " --> pdb=" O VAL E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 231 removed outlier: 3.509A pdb=" N LEU E 227 " --> pdb=" O HIS E 223 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 288 removed outlier: 3.949A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 331 removed outlier: 3.543A pdb=" N CYS E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 344 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 352 through 370 removed outlier: 3.783A pdb=" N THR E 356 " --> pdb=" O LEU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 420 Proline residue: E 412 - end of helix Processing helix chain 'E' and resid 430 through 445 Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.647A pdb=" N ASP E 456 " --> pdb=" O ASP E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 474 removed outlier: 3.798A pdb=" N LEU E 466 " --> pdb=" O TYR E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 488 removed outlier: 4.218A pdb=" N GLN E 482 " --> pdb=" O PRO E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 518 removed outlier: 4.372A pdb=" N LEU E 515 " --> pdb=" O PRO E 511 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN E 518 " --> pdb=" O PRO E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 523 removed outlier: 3.545A pdb=" N ASP E 523 " --> pdb=" O ILE E 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 520 through 523' Processing helix chain 'E' and resid 524 through 530 Processing helix chain 'E' and resid 549 through 572 removed outlier: 3.896A pdb=" N GLN E 553 " --> pdb=" O GLN E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 587 Processing helix chain 'E' and resid 620 through 628 removed outlier: 4.119A pdb=" N ALA E 624 " --> pdb=" O PRO E 620 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN E 625 " --> pdb=" O PRO E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 709 Processing helix chain 'E' and resid 736 through 746 Processing helix chain 'E' and resid 748 through 771 Processing helix chain 'E' and resid 772 through 773 No H-bonds generated for 'chain 'E' and resid 772 through 773' Processing helix chain 'E' and resid 774 through 780 removed outlier: 3.539A pdb=" N HIS E 777 " --> pdb=" O ARG E 774 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS E 779 " --> pdb=" O ALA E 776 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 796 removed outlier: 3.635A pdb=" N LEU E 785 " --> pdb=" O LEU E 781 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR E 796 " --> pdb=" O GLN E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 801 through 817 removed outlier: 4.509A pdb=" N ASN E 805 " --> pdb=" O ARG E 801 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY E 806 " --> pdb=" O SER E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 824 through 828 removed outlier: 3.737A pdb=" N HIS E 828 " --> pdb=" O GLU E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 839 through 864 removed outlier: 3.699A pdb=" N VAL E 843 " --> pdb=" O ASP E 839 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU E 844 " --> pdb=" O PRO E 840 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 845 " --> pdb=" O PHE E 841 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR E 850 " --> pdb=" O SER E 846 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE E 851 " --> pdb=" O LEU E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 882 through 887 Processing helix chain 'E' and resid 896 through 904 Processing helix chain 'E' and resid 927 through 944 Processing helix chain 'E' and resid 951 through 968 removed outlier: 4.032A pdb=" N GLN E 957 " --> pdb=" O GLN E 953 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 709 Processing helix chain 'F' and resid 728 through 733 Processing helix chain 'F' and resid 739 through 746 Processing helix chain 'F' and resid 748 through 773 removed outlier: 3.710A pdb=" N VAL F 760 " --> pdb=" O ALA F 756 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU F 771 " --> pdb=" O GLN F 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 794 removed outlier: 5.026A pdb=" N GLN F 783 " --> pdb=" O LYS F 779 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR F 784 " --> pdb=" O GLN F 780 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS F 794 " --> pdb=" O LYS F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 800 through 817 removed outlier: 3.524A pdb=" N LEU F 804 " --> pdb=" O LYS F 800 " (cutoff:3.500A) Processing helix chain 'F' and resid 818 through 822 Processing helix chain 'F' and resid 839 through 863 removed outlier: 3.741A pdb=" N VAL F 843 " --> pdb=" O ASP F 839 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F 863 " --> pdb=" O ILE F 859 " (cutoff:3.500A) Processing helix chain 'F' and resid 880 through 887 Processing helix chain 'F' and resid 891 through 904 removed outlier: 3.814A pdb=" N GLU F 895 " --> pdb=" O ARG F 891 " (cutoff:3.500A) Processing helix chain 'F' and resid 908 through 910 No H-bonds generated for 'chain 'F' and resid 908 through 910' Processing helix chain 'F' and resid 927 through 944 Processing helix chain 'F' and resid 950 through 969 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.486A pdb=" N ARG A 29 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLU A 36 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 31 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 34 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 68 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 80 " --> pdb=" O PHE A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.560A pdb=" N HIS A 80 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS B 3 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 53 Processing sheet with id=AA4, first strand: chain 'C' and resid 235 through 244 removed outlier: 5.682A pdb=" N ILE C 236 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER C 268 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N HIS C 238 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLY C 263 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 161 " --> pdb=" O LYS C 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 391 through 394 removed outlier: 3.508A pdb=" N HIS C 492 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 580 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 533 through 538 removed outlier: 4.111A pdb=" N ILE C 544 " --> pdb=" O TYR C 450 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 652 through 656 removed outlier: 6.986A pdb=" N THR C 652 " --> pdb=" O HIS C 688 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL C 690 " --> pdb=" O THR C 652 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU C 654 " --> pdb=" O VAL C 690 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 692 " --> pdb=" O LEU C 654 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU C 656 " --> pdb=" O LEU C 692 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 713 " --> pdb=" O VAL C 726 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY C 724 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY F 724 " --> pdb=" O ILE F 715 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N HIS F 714 " --> pdb=" O HIS F 688 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL F 690 " --> pdb=" O HIS F 714 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA F 716 " --> pdb=" O VAL F 690 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU F 692 " --> pdb=" O ALA F 716 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N THR F 652 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA F 689 " --> pdb=" O THR F 652 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 677 through 683 removed outlier: 6.419A pdb=" N VAL C 672 " --> pdb=" O THR C 679 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS C 681 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU C 670 " --> pdb=" O LYS C 681 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 912 through 916 Processing sheet with id=AB1, first strand: chain 'D' and resid 652 through 656 removed outlier: 5.724A pdb=" N THR D 652 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 689 " --> pdb=" O THR D 652 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N HIS D 714 " --> pdb=" O HIS D 688 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 690 " --> pdb=" O HIS D 714 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA D 716 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU D 692 " --> pdb=" O ALA D 716 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 724 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 724 " --> pdb=" O ILE E 715 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E 713 " --> pdb=" O VAL E 726 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR E 652 " --> pdb=" O HIS E 688 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL E 690 " --> pdb=" O THR E 652 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU E 654 " --> pdb=" O VAL E 690 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU E 692 " --> pdb=" O LEU E 654 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU E 656 " --> pdb=" O LEU E 692 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 677 through 683 removed outlier: 5.397A pdb=" N ILE D 678 " --> pdb=" O LYS D 674 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS D 674 " --> pdb=" O ILE D 678 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 912 through 916 Processing sheet with id=AB4, first strand: chain 'E' and resid 50 through 53 Processing sheet with id=AB5, first strand: chain 'E' and resid 235 through 244 removed outlier: 5.682A pdb=" N ILE E 236 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER E 268 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS E 238 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR E 266 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLY E 263 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN E 161 " --> pdb=" O LYS E 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 391 through 394 removed outlier: 3.508A pdb=" N HIS E 492 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 580 " --> pdb=" O GLU E 499 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 533 through 538 removed outlier: 4.111A pdb=" N ILE E 544 " --> pdb=" O TYR E 450 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 677 through 683 removed outlier: 6.419A pdb=" N VAL E 672 " --> pdb=" O THR E 679 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS E 681 " --> pdb=" O LEU E 670 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU E 670 " --> pdb=" O LYS E 681 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 912 through 916 Processing sheet with id=AC1, first strand: chain 'F' and resid 677 through 683 removed outlier: 5.397A pdb=" N ILE F 678 " --> pdb=" O LYS F 674 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS F 674 " --> pdb=" O ILE F 678 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 912 through 916 1021 hydrogen bonds defined for protein. 2913 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.70 Time building geometry restraints manager: 8.96 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: 6774 1.34 - 1.45: 3211 1.45 - 1.57: 12265 1.57 - 1.69: 2 1.69 - 1.81: 80 Bond restraints: 22332 Sorted by residual: bond pdb=" N GLN A 89 " pdb=" CA GLN A 89 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.23e-02 6.61e+03 6.07e+00 bond pdb=" CB VAL C 713 " pdb=" CG1 VAL C 713 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.36e+00 bond pdb=" CB VAL E 713 " pdb=" CG1 VAL E 713 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.12e+00 bond pdb=" CB VAL E 690 " pdb=" CG1 VAL E 690 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CB LYS C 346 " pdb=" CG LYS C 346 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.35e+00 ... (remaining 22327 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.43: 346 105.43 - 112.60: 11681 112.60 - 119.77: 7413 119.77 - 126.94: 10390 126.94 - 134.11: 344 Bond angle restraints: 30174 Sorted by residual: angle pdb=" C GLU C 979 " pdb=" N LEU C 980 " pdb=" CA LEU C 980 " ideal model delta sigma weight residual 120.82 126.61 -5.79 1.47e+00 4.63e-01 1.55e+01 angle pdb=" C GLU E 979 " pdb=" N LEU E 980 " pdb=" CA LEU E 980 " ideal model delta sigma weight residual 120.82 126.57 -5.75 1.47e+00 4.63e-01 1.53e+01 angle pdb=" C ASP D 666 " pdb=" N ASN D 667 " pdb=" CA ASN D 667 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.53e+01 angle pdb=" C ASP F 666 " pdb=" N ASN F 667 " pdb=" CA ASN F 667 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N LEU C 919 " pdb=" CA LEU C 919 " pdb=" C LEU C 919 " ideal model delta sigma weight residual 114.75 109.96 4.79 1.26e+00 6.30e-01 1.45e+01 ... (remaining 30169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 12009 17.86 - 35.72: 1199 35.72 - 53.59: 195 53.59 - 71.45: 41 71.45 - 89.31: 10 Dihedral angle restraints: 13454 sinusoidal: 5606 harmonic: 7848 Sorted by residual: dihedral pdb=" CA ARG C 891 " pdb=" C ARG C 891 " pdb=" N HIS C 892 " pdb=" CA HIS C 892 " ideal model delta harmonic sigma weight residual 180.00 158.43 21.57 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG E 891 " pdb=" C ARG E 891 " pdb=" N HIS E 892 " pdb=" CA HIS E 892 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG D 835 " pdb=" C ARG D 835 " pdb=" N PRO D 836 " pdb=" CA PRO D 836 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 13451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2734 0.064 - 0.129: 517 0.129 - 0.193: 58 0.193 - 0.257: 2 0.257 - 0.322: 1 Chirality restraints: 3312 Sorted by residual: chirality pdb=" CB ILE A 66 " pdb=" CA ILE A 66 " pdb=" CG1 ILE A 66 " pdb=" CG2 ILE A 66 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CG LEU C 36 " pdb=" CB LEU C 36 " pdb=" CD1 LEU C 36 " pdb=" CD2 LEU C 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU E 36 " pdb=" CB LEU E 36 " pdb=" CD1 LEU E 36 " pdb=" CD2 LEU E 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3309 not shown) Planarity restraints: 3870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 41 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO A 42 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 42 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 42 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 477 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.67e+00 pdb=" N PRO C 478 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 478 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 478 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 477 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO E 478 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 478 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 478 " -0.036 5.00e-02 4.00e+02 ... (remaining 3867 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 6 2.22 - 2.89: 7834 2.89 - 3.56: 28885 3.56 - 4.23: 45548 4.23 - 4.90: 82294 Nonbonded interactions: 164567 Sorted by model distance: nonbonded pdb=" CE1 TYR A 50 " pdb=" CG GLN E 554 " model vdw 1.548 3.740 nonbonded pdb=" CD1 TYR A 50 " pdb=" CG GLN E 554 " model vdw 1.892 3.740 nonbonded pdb=" NZ LYS A 25 " pdb=" OE1 GLN C 668 " model vdw 1.909 2.520 nonbonded pdb=" O LEU D 723 " pdb=" OG SER E 728 " model vdw 2.124 2.440 nonbonded pdb=" OD1 ASN A 65 " pdb=" NE2 GLN B 31 " model vdw 2.185 2.520 ... (remaining 164562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 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: 0.030 Extract box with map and model: 13.590 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 56.790 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 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 : 0.006 0.076 22332 Z= 0.364 Angle : 0.829 8.962 30174 Z= 0.471 Chirality : 0.050 0.322 3312 Planarity : 0.006 0.068 3870 Dihedral : 14.440 89.310 8362 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 2638 helix: 0.28 (0.15), residues: 1192 sheet: -0.22 (0.31), residues: 280 loop : -1.86 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 162 HIS 0.009 0.001 HIS A 53 PHE 0.020 0.002 PHE D 819 TYR 0.021 0.002 TYR F 815 ARG 0.028 0.001 ARG E 834 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7625 (ttpt) REVERT: A 53 HIS cc_start: 0.7879 (m-70) cc_final: 0.7557 (m-70) REVERT: A 87 ILE cc_start: 0.8549 (pt) cc_final: 0.8286 (tp) REVERT: A 96 LEU cc_start: 0.8566 (tp) cc_final: 0.8292 (tp) REVERT: B 90 LEU cc_start: 0.8775 (mt) cc_final: 0.8156 (mt) REVERT: C 40 LEU cc_start: 0.7401 (tp) cc_final: 0.6205 (tt) REVERT: C 327 LEU cc_start: 0.8108 (tp) cc_final: 0.7895 (pp) REVERT: C 389 GLU cc_start: 0.2834 (mt-10) cc_final: 0.1995 (tp30) REVERT: C 411 THR cc_start: 0.8080 (m) cc_final: 0.7839 (m) REVERT: C 417 ILE cc_start: 0.8463 (tp) cc_final: 0.8107 (tp) REVERT: C 444 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6947 (mp10) REVERT: C 564 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7861 (tmmt) REVERT: C 722 TYR cc_start: 0.4874 (t80) cc_final: 0.4623 (t80) REVERT: C 731 PRO cc_start: 0.7860 (Cg_exo) cc_final: 0.7615 (Cg_endo) REVERT: C 748 ARG cc_start: 0.6962 (mtt-85) cc_final: 0.6727 (ttt180) REVERT: C 759 ILE cc_start: 0.7769 (mt) cc_final: 0.7078 (tp) REVERT: C 784 THR cc_start: 0.6058 (m) cc_final: 0.5662 (p) REVERT: C 794 LYS cc_start: 0.7218 (mtpt) cc_final: 0.6905 (tptp) REVERT: C 819 PHE cc_start: 0.6796 (m-10) cc_final: 0.6520 (m-80) REVERT: C 874 GLN cc_start: 0.7813 (mt0) cc_final: 0.7573 (mt0) REVERT: C 924 ILE cc_start: 0.5345 (mp) cc_final: 0.4407 (tt) REVERT: C 966 MET cc_start: 0.7446 (mtp) cc_final: 0.7242 (mtt) REVERT: D 745 MET cc_start: 0.8544 (mmt) cc_final: 0.8139 (mmt) REVERT: D 979 GLU cc_start: 0.8726 (tt0) cc_final: 0.8513 (tt0) REVERT: E 261 MET cc_start: 0.6345 (ptm) cc_final: 0.5748 (mmm) REVERT: E 280 MET cc_start: -0.7255 (mtp) cc_final: -0.7593 (mmt) REVERT: E 853 TYR cc_start: 0.8494 (t80) cc_final: 0.8228 (t80) REVERT: F 676 ASP cc_start: 0.6563 (m-30) cc_final: 0.6109 (t70) REVERT: F 719 THR cc_start: 0.8605 (p) cc_final: 0.8260 (t) REVERT: F 792 GLN cc_start: 0.8470 (tt0) cc_final: 0.8256 (tt0) REVERT: F 813 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.8223 (tpt90) REVERT: F 956 TYR cc_start: 0.7253 (t80) cc_final: 0.6767 (t80) REVERT: F 967 HIS cc_start: 0.8697 (t-90) cc_final: 0.8429 (t70) REVERT: F 973 GLN cc_start: 0.8217 (mt0) cc_final: 0.7907 (mt0) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.3997 time to fit residues: 291.1765 Evaluate side-chains 218 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.6980 chunk 200 optimal weight: 0.0060 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 206 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 239 optimal weight: 0.0050 overall best weight: 0.4410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 83 ASN A 89 GLN B 54 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN C 447 HIS C 653 HIS C 730 GLN C 734 ASN C 767 GLN C 817 GLN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 554 GLN E 973 GLN F 733 GLN F 817 GLN F 969 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22332 Z= 0.192 Angle : 0.615 8.848 30174 Z= 0.322 Chirality : 0.043 0.201 3312 Planarity : 0.005 0.080 3870 Dihedral : 4.856 21.065 2910 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.95 % Allowed : 9.51 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2638 helix: 1.08 (0.15), residues: 1204 sheet: 0.14 (0.31), residues: 290 loop : -1.50 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 85 HIS 0.014 0.001 HIS F 828 PHE 0.015 0.002 PHE C 822 TYR 0.019 0.001 TYR F 815 ARG 0.012 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 234 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7283 (mp0) REVERT: A 79 SER cc_start: 0.9279 (m) cc_final: 0.9046 (p) REVERT: A 87 ILE cc_start: 0.8391 (pt) cc_final: 0.8102 (tp) REVERT: B 26 TYR cc_start: 0.8960 (m-80) cc_final: 0.8687 (m-80) REVERT: B 44 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7771 (mmm-85) REVERT: C 389 GLU cc_start: 0.3320 (mt-10) cc_final: 0.1757 (tp30) REVERT: C 411 THR cc_start: 0.8099 (m) cc_final: 0.7883 (m) REVERT: C 417 ILE cc_start: 0.8570 (tp) cc_final: 0.8160 (tp) REVERT: C 520 ILE cc_start: 0.9055 (tt) cc_final: 0.8842 (tt) REVERT: C 564 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7931 (tmmt) REVERT: C 641 LYS cc_start: 0.5960 (ptpt) cc_final: 0.5759 (pttt) REVERT: C 731 PRO cc_start: 0.7946 (Cg_exo) cc_final: 0.7633 (Cg_endo) REVERT: C 748 ARG cc_start: 0.6999 (mtt-85) cc_final: 0.6719 (ttt180) REVERT: C 887 MET cc_start: 0.8520 (ttp) cc_final: 0.8149 (ttp) REVERT: D 745 MET cc_start: 0.8575 (mmt) cc_final: 0.8123 (mmt) REVERT: D 966 MET cc_start: 0.8316 (mtt) cc_final: 0.8091 (mtt) REVERT: E 280 MET cc_start: -0.7666 (mtp) cc_final: -0.8003 (mmt) REVERT: E 887 MET cc_start: 0.8103 (ptm) cc_final: 0.7872 (ppp) REVERT: E 970 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: F 719 THR cc_start: 0.8328 (p) cc_final: 0.8076 (t) REVERT: F 745 MET cc_start: 0.7590 (tpp) cc_final: 0.7345 (tpp) REVERT: F 813 ARG cc_start: 0.8502 (ttp-110) cc_final: 0.8186 (tpt90) REVERT: F 845 LEU cc_start: 0.8671 (mt) cc_final: 0.8089 (pp) REVERT: F 956 TYR cc_start: 0.7375 (t80) cc_final: 0.6859 (t80) REVERT: F 970 GLN cc_start: 0.6971 (tm-30) cc_final: 0.6301 (tm-30) REVERT: F 980 LEU cc_start: 0.5916 (mt) cc_final: 0.5669 (tp) outliers start: 46 outliers final: 28 residues processed: 268 average time/residue: 0.3592 time to fit residues: 146.7446 Evaluate side-chains 214 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 738 ASN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 817 GLN Chi-restraints excluded: chain C residue 946 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 471 LYS Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 970 GLN Chi-restraints excluded: chain F residue 760 VAL Chi-restraints excluded: chain F residue 826 TRP Chi-restraints excluded: chain F residue 854 SER Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 240 optimal weight: 0.7980 chunk 259 optimal weight: 5.9990 chunk 213 optimal weight: 0.7980 chunk 238 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 12 HIS B 54 GLN C 334 HIS C 444 GLN C 576 HIS C 632 GLN C 686 GLN C 817 GLN C 855 HIS C 953 GLN D 668 GLN E 334 HIS E 518 ASN E 842 ASN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 921 GLN F 714 HIS ** F 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 792 GLN F 952 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22332 Z= 0.311 Angle : 0.648 8.888 30174 Z= 0.343 Chirality : 0.046 0.211 3312 Planarity : 0.005 0.063 3870 Dihedral : 4.868 20.730 2910 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.38 % Allowed : 13.46 % Favored : 84.17 % 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: 0.01 (0.16), residues: 2638 helix: 1.26 (0.15), residues: 1196 sheet: 0.24 (0.31), residues: 300 loop : -1.45 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 162 HIS 0.010 0.001 HIS E 550 PHE 0.026 0.002 PHE C 816 TYR 0.026 0.002 TYR C 722 ARG 0.006 0.001 ARG C 931 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 199 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7603 (mp0) REVERT: A 49 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7977 (mt-10) REVERT: A 50 TYR cc_start: 0.7702 (t80) cc_final: 0.7152 (t80) REVERT: A 53 HIS cc_start: 0.8027 (m170) cc_final: 0.7575 (m170) REVERT: A 89 GLN cc_start: 0.5403 (OUTLIER) cc_final: 0.3633 (mm110) REVERT: B 9 ASP cc_start: 0.7244 (t0) cc_final: 0.7019 (t0) REVERT: B 12 HIS cc_start: 0.7830 (t-170) cc_final: 0.7566 (t-90) REVERT: B 44 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7849 (mmm-85) REVERT: C 389 GLU cc_start: 0.3606 (mt-10) cc_final: 0.1320 (tp30) REVERT: C 564 LYS cc_start: 0.8354 (ttpt) cc_final: 0.8065 (ttpt) REVERT: C 641 LYS cc_start: 0.6450 (ptpt) cc_final: 0.6214 (ptmt) REVERT: D 779 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8408 (ptmt) REVERT: E 261 MET cc_start: 0.6301 (ptm) cc_final: 0.5765 (mmm) REVERT: E 280 MET cc_start: -0.7331 (mtp) cc_final: -0.7662 (mmt) REVERT: E 813 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7652 (ttm110) REVERT: E 887 MET cc_start: 0.8074 (ptm) cc_final: 0.7778 (ppp) REVERT: F 719 THR cc_start: 0.8507 (p) cc_final: 0.8237 (t) REVERT: F 745 MET cc_start: 0.8244 (tpp) cc_final: 0.7928 (tpp) REVERT: F 813 ARG cc_start: 0.8564 (ttp-110) cc_final: 0.8184 (tpt90) REVERT: F 845 LEU cc_start: 0.8702 (mt) cc_final: 0.8232 (pp) REVERT: F 970 GLN cc_start: 0.6741 (tm-30) cc_final: 0.6169 (tm-30) REVERT: F 973 GLN cc_start: 0.8418 (mt0) cc_final: 0.7923 (mt0) outliers start: 56 outliers final: 31 residues processed: 240 average time/residue: 0.3887 time to fit residues: 145.0357 Evaluate side-chains 207 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 953 GLN Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 471 LYS Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 760 VAL Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 0.2980 chunk 255 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 228 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 667 ASN C 730 GLN C 734 ASN C 953 GLN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 767 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22332 Z= 0.173 Angle : 0.554 9.506 30174 Z= 0.289 Chirality : 0.042 0.178 3312 Planarity : 0.004 0.067 3870 Dihedral : 4.544 21.289 2910 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.42 % Allowed : 14.64 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2638 helix: 1.68 (0.16), residues: 1184 sheet: 0.15 (0.31), residues: 312 loop : -1.31 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 739 HIS 0.008 0.001 HIS E 550 PHE 0.013 0.001 PHE E 70 TYR 0.016 0.001 TYR C 722 ARG 0.010 0.000 ARG C 801 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 201 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8942 (mmtp) cc_final: 0.8376 (mmmt) REVERT: A 24 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7535 (mp0) REVERT: A 49 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7826 (mt-10) REVERT: A 50 TYR cc_start: 0.7668 (t80) cc_final: 0.7252 (t80) REVERT: A 53 HIS cc_start: 0.7698 (m170) cc_final: 0.7144 (m90) REVERT: B 12 HIS cc_start: 0.7802 (t-170) cc_final: 0.7407 (t-90) REVERT: B 44 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7757 (mmm-85) REVERT: C 35 PHE cc_start: 0.8222 (t80) cc_final: 0.7534 (m-80) REVERT: C 389 GLU cc_start: 0.3540 (mt-10) cc_final: 0.1288 (tp30) REVERT: C 417 ILE cc_start: 0.8574 (tp) cc_final: 0.8061 (tp) REVERT: C 564 LYS cc_start: 0.8282 (ttpt) cc_final: 0.7991 (tmmt) REVERT: C 641 LYS cc_start: 0.6423 (ptpt) cc_final: 0.6081 (ptmt) REVERT: C 897 TYR cc_start: 0.7962 (t80) cc_final: 0.7733 (t80) REVERT: C 966 MET cc_start: 0.7554 (mpp) cc_final: 0.6566 (mpp) REVERT: D 745 MET cc_start: 0.8675 (mmt) cc_final: 0.8347 (mmt) REVERT: D 815 TYR cc_start: 0.7258 (t80) cc_final: 0.7049 (t80) REVERT: E 261 MET cc_start: 0.6294 (ptm) cc_final: 0.5803 (tpp) REVERT: E 280 MET cc_start: -0.7415 (mtp) cc_final: -0.7685 (mmt) REVERT: E 553 GLN cc_start: 0.4174 (OUTLIER) cc_final: 0.3918 (mp10) REVERT: E 631 PRO cc_start: 0.6640 (Cg_endo) cc_final: 0.6426 (Cg_exo) REVERT: E 813 ARG cc_start: 0.7926 (ttm110) cc_final: 0.7701 (ttm110) REVERT: E 887 MET cc_start: 0.8299 (ptm) cc_final: 0.7975 (ppp) REVERT: F 719 THR cc_start: 0.8497 (p) cc_final: 0.8254 (t) REVERT: F 745 MET cc_start: 0.8212 (tpp) cc_final: 0.7969 (tpp) REVERT: F 813 ARG cc_start: 0.8420 (ttp-110) cc_final: 0.8128 (tpt90) REVERT: F 845 LEU cc_start: 0.8687 (mt) cc_final: 0.8222 (pp) REVERT: F 887 MET cc_start: 0.6859 (ptm) cc_final: 0.6659 (ptm) REVERT: F 970 GLN cc_start: 0.6746 (tm-30) cc_final: 0.6489 (tm-30) REVERT: F 973 GLN cc_start: 0.8400 (mt0) cc_final: 0.7939 (mt0) outliers start: 57 outliers final: 38 residues processed: 246 average time/residue: 0.3326 time to fit residues: 128.7042 Evaluate side-chains 220 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 953 GLN Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 471 LYS Chi-restraints excluded: chain E residue 553 GLN Chi-restraints excluded: chain E residue 652 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 967 HIS Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 190 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 217 optimal weight: 0.6980 chunk 176 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 86 HIS C 632 GLN C 973 GLN D 767 GLN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22332 Z= 0.211 Angle : 0.558 11.000 30174 Z= 0.291 Chirality : 0.042 0.153 3312 Planarity : 0.004 0.066 3870 Dihedral : 4.486 20.149 2910 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.14 % Allowed : 15.53 % Favored : 81.32 % 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: 0.40 (0.17), residues: 2638 helix: 1.74 (0.16), residues: 1186 sheet: 0.07 (0.31), residues: 308 loop : -1.30 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 162 HIS 0.010 0.001 HIS C 918 PHE 0.013 0.001 PHE E 70 TYR 0.016 0.001 TYR C 722 ARG 0.006 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 193 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.6710 (p0) cc_final: 0.6483 (p0) REVERT: A 18 LYS cc_start: 0.8982 (mmtp) cc_final: 0.8409 (mmmt) REVERT: A 24 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7497 (mp0) REVERT: A 49 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 50 TYR cc_start: 0.7897 (t80) cc_final: 0.7235 (t80) REVERT: A 53 HIS cc_start: 0.7712 (m170) cc_final: 0.7190 (m170) REVERT: A 54 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8142 (mm-40) REVERT: B 9 ASP cc_start: 0.7077 (t0) cc_final: 0.6841 (t0) REVERT: B 26 TYR cc_start: 0.9042 (m-80) cc_final: 0.8740 (m-80) REVERT: B 44 ARG cc_start: 0.8082 (mtp85) cc_final: 0.7790 (mmm-85) REVERT: B 65 ASN cc_start: 0.8806 (t0) cc_final: 0.8391 (p0) REVERT: C 35 PHE cc_start: 0.8251 (t80) cc_final: 0.7591 (m-80) REVERT: C 564 LYS cc_start: 0.8305 (ttpt) cc_final: 0.8036 (tmmt) REVERT: C 641 LYS cc_start: 0.6444 (ptpt) cc_final: 0.6221 (ptmt) REVERT: C 887 MET cc_start: 0.8237 (tmm) cc_final: 0.7950 (tmm) REVERT: C 938 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8653 (tt) REVERT: C 966 MET cc_start: 0.7712 (mpp) cc_final: 0.6923 (mpp) REVERT: D 745 MET cc_start: 0.8591 (mmt) cc_final: 0.8257 (mmt) REVERT: D 771 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8123 (mt) REVERT: E 261 MET cc_start: 0.6230 (ptm) cc_final: 0.5782 (tpp) REVERT: E 280 MET cc_start: -0.7280 (mtp) cc_final: -0.7596 (mmt) REVERT: E 286 MET cc_start: 0.5122 (mpp) cc_final: 0.4553 (pmm) REVERT: E 813 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7740 (ttm110) REVERT: E 887 MET cc_start: 0.8320 (ptm) cc_final: 0.8015 (ppp) REVERT: F 813 ARG cc_start: 0.8478 (ttp-110) cc_final: 0.8115 (tpt90) REVERT: F 845 LEU cc_start: 0.8662 (mt) cc_final: 0.8171 (pp) REVERT: F 852 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7881 (mm) REVERT: F 973 GLN cc_start: 0.8408 (mt0) cc_final: 0.7963 (mt0) outliers start: 74 outliers final: 50 residues processed: 248 average time/residue: 0.3354 time to fit residues: 131.4061 Evaluate side-chains 228 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 175 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 738 ASN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 918 HIS Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 471 LYS Chi-restraints excluded: chain E residue 652 THR Chi-restraints excluded: chain E residue 699 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 927 SER Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 793 TYR Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 852 LEU Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 0.0050 chunk 134 optimal weight: 5.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 148 HIS C 285 GLN C 561 GLN C 680 HIS C 953 GLN ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22332 Z= 0.261 Angle : 0.580 7.449 30174 Z= 0.303 Chirality : 0.043 0.158 3312 Planarity : 0.004 0.067 3870 Dihedral : 4.558 19.840 2910 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.27 % Allowed : 16.51 % Favored : 80.22 % 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: 0.29 (0.17), residues: 2638 helix: 1.64 (0.16), residues: 1188 sheet: -0.14 (0.32), residues: 292 loop : -1.29 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 739 HIS 0.006 0.001 HIS B 53 PHE 0.013 0.001 PHE E 70 TYR 0.019 0.002 TYR F 815 ARG 0.004 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 174 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.9005 (mmtp) cc_final: 0.8449 (mmmt) REVERT: A 24 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7502 (mp0) REVERT: A 49 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7876 (mt-10) REVERT: A 50 TYR cc_start: 0.7931 (t80) cc_final: 0.7372 (t80) REVERT: A 53 HIS cc_start: 0.7812 (m170) cc_final: 0.7249 (m90) REVERT: A 54 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8471 (mm-40) REVERT: B 9 ASP cc_start: 0.6822 (t0) cc_final: 0.6591 (t0) REVERT: B 12 HIS cc_start: 0.7903 (t-90) cc_final: 0.7597 (t-90) REVERT: B 44 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7911 (mmm-85) REVERT: C 35 PHE cc_start: 0.8252 (t80) cc_final: 0.7557 (m-80) REVERT: C 564 LYS cc_start: 0.8335 (ttpt) cc_final: 0.8062 (tmmt) REVERT: C 887 MET cc_start: 0.8332 (tmm) cc_final: 0.7768 (tmm) REVERT: C 897 TYR cc_start: 0.8227 (t80) cc_final: 0.7950 (t80) REVERT: C 957 GLN cc_start: 0.8296 (tp40) cc_final: 0.7660 (tp-100) REVERT: C 966 MET cc_start: 0.7916 (mpp) cc_final: 0.7211 (mpp) REVERT: D 745 MET cc_start: 0.8534 (mmt) cc_final: 0.8188 (mmt) REVERT: D 966 MET cc_start: 0.8475 (mtt) cc_final: 0.8192 (mtt) REVERT: E 141 MET cc_start: 0.1250 (mpp) cc_final: 0.0432 (ttm) REVERT: E 261 MET cc_start: 0.6108 (ptm) cc_final: 0.5670 (tpp) REVERT: E 280 MET cc_start: -0.7334 (mtp) cc_final: -0.7557 (mmt) REVERT: E 813 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7741 (ttm110) REVERT: E 887 MET cc_start: 0.8235 (ptm) cc_final: 0.7892 (ppp) REVERT: F 813 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8047 (tpt90) REVERT: F 845 LEU cc_start: 0.8644 (mt) cc_final: 0.8133 (pp) REVERT: F 970 GLN cc_start: 0.6817 (tm-30) cc_final: 0.6544 (tm-30) outliers start: 77 outliers final: 55 residues processed: 233 average time/residue: 0.3195 time to fit residues: 118.1760 Evaluate side-chains 219 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 164 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 918 HIS Chi-restraints excluded: chain C residue 953 GLN Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 471 LYS Chi-restraints excluded: chain E residue 652 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 879 HIS Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 927 SER Chi-restraints excluded: chain E residue 948 ASP Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 793 TYR Chi-restraints excluded: chain F residue 839 ASP Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 854 SER Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 186 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 143 GLN C 285 GLN C 667 ASN C 680 HIS C 961 GLN ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 873 HIS ** F 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22332 Z= 0.220 Angle : 0.562 10.484 30174 Z= 0.293 Chirality : 0.043 0.161 3312 Planarity : 0.004 0.068 3870 Dihedral : 4.494 19.671 2910 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.40 % Allowed : 16.89 % Favored : 79.71 % 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: 0.38 (0.17), residues: 2638 helix: 1.72 (0.16), residues: 1190 sheet: -0.11 (0.31), residues: 310 loop : -1.27 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 739 HIS 0.011 0.001 HIS C 952 PHE 0.014 0.001 PHE F 751 TYR 0.017 0.001 TYR E 201 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 180 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8991 (mmtp) cc_final: 0.8476 (mmmt) REVERT: A 24 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7581 (mp0) REVERT: A 49 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8211 (mt-10) REVERT: A 50 TYR cc_start: 0.7935 (t80) cc_final: 0.7432 (t80) REVERT: A 54 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8547 (mm-40) REVERT: B 9 ASP cc_start: 0.6986 (t0) cc_final: 0.6588 (t0) REVERT: B 12 HIS cc_start: 0.7807 (t-90) cc_final: 0.7492 (t-90) REVERT: B 19 LEU cc_start: 0.9162 (mp) cc_final: 0.8960 (mp) REVERT: B 26 TYR cc_start: 0.9054 (m-80) cc_final: 0.8748 (m-80) REVERT: B 44 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7892 (mmm-85) REVERT: B 65 ASN cc_start: 0.8247 (p0) cc_final: 0.7967 (p0) REVERT: C 35 PHE cc_start: 0.8254 (t80) cc_final: 0.7558 (m-80) REVERT: C 564 LYS cc_start: 0.8342 (ttpt) cc_final: 0.8089 (tmmt) REVERT: C 887 MET cc_start: 0.8364 (tmm) cc_final: 0.7825 (tmm) REVERT: C 897 TYR cc_start: 0.8232 (t80) cc_final: 0.7940 (t80) REVERT: C 957 GLN cc_start: 0.8438 (tp40) cc_final: 0.7653 (tp-100) REVERT: C 961 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: C 966 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7297 (mpp) REVERT: D 745 MET cc_start: 0.8575 (mmt) cc_final: 0.8195 (mmt) REVERT: D 814 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7497 (mp0) REVERT: D 966 MET cc_start: 0.8452 (mtt) cc_final: 0.8167 (mtt) REVERT: E 261 MET cc_start: 0.6050 (ptm) cc_final: 0.5459 (mtp) REVERT: E 280 MET cc_start: -0.7215 (mtp) cc_final: -0.7468 (mmt) REVERT: E 418 MET cc_start: 0.3115 (ptp) cc_final: 0.2689 (tpp) REVERT: E 813 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7817 (ttm110) REVERT: E 887 MET cc_start: 0.8372 (ptm) cc_final: 0.8053 (ppp) REVERT: F 745 MET cc_start: 0.7974 (tpp) cc_final: 0.7644 (tpp) REVERT: F 813 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8048 (tpt90) REVERT: F 828 HIS cc_start: 0.8053 (m90) cc_final: 0.7590 (m-70) REVERT: F 845 LEU cc_start: 0.8652 (mt) cc_final: 0.8137 (pp) REVERT: F 909 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7074 (mp10) REVERT: F 970 GLN cc_start: 0.6811 (tm-30) cc_final: 0.6514 (tm-30) outliers start: 80 outliers final: 60 residues processed: 241 average time/residue: 0.3240 time to fit residues: 124.4545 Evaluate side-chains 237 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 174 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 918 HIS Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 953 GLN Chi-restraints excluded: chain C residue 961 GLN Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 652 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 879 HIS Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 927 SER Chi-restraints excluded: chain E residue 948 ASP Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain F residue 668 GLN Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 793 TYR Chi-restraints excluded: chain F residue 819 PHE Chi-restraints excluded: chain F residue 839 ASP Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 909 GLN Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN C 324 GLN C 447 HIS ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 GLN C 968 ASN E 111 ASN ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 734 ASN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 954 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 22332 Z= 0.337 Angle : 0.641 8.435 30174 Z= 0.338 Chirality : 0.046 0.183 3312 Planarity : 0.005 0.068 3870 Dihedral : 4.908 19.863 2910 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.23 % Allowed : 17.36 % Favored : 79.41 % 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: 0.01 (0.17), residues: 2638 helix: 1.36 (0.15), residues: 1186 sheet: -0.10 (0.31), residues: 290 loop : -1.44 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 226 HIS 0.007 0.001 HIS E 653 PHE 0.016 0.002 PHE E 35 TYR 0.021 0.002 TYR A 26 ARG 0.006 0.001 ARG E 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 181 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8994 (mmtp) cc_final: 0.8488 (mmmt) REVERT: A 24 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7677 (mp0) REVERT: A 49 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 53 HIS cc_start: 0.8161 (m170) cc_final: 0.7638 (m90) REVERT: A 54 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8479 (mm-40) REVERT: B 12 HIS cc_start: 0.7874 (t-90) cc_final: 0.7588 (t-90) REVERT: B 44 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7914 (mmm-85) REVERT: C 564 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8107 (tmmt) REVERT: C 887 MET cc_start: 0.8417 (tmm) cc_final: 0.7836 (tmm) REVERT: C 957 GLN cc_start: 0.8023 (tp40) cc_final: 0.7590 (tp-100) REVERT: C 961 GLN cc_start: 0.8358 (mt0) cc_final: 0.7959 (mt0) REVERT: C 966 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7435 (mpp) REVERT: D 709 HIS cc_start: 0.9186 (OUTLIER) cc_final: 0.8718 (m-70) REVERT: D 966 MET cc_start: 0.8473 (mtt) cc_final: 0.8201 (mtt) REVERT: E 141 MET cc_start: 0.0448 (mpp) cc_final: -0.0517 (ttm) REVERT: E 261 MET cc_start: 0.5761 (ptm) cc_final: 0.5262 (mtp) REVERT: E 418 MET cc_start: 0.3410 (ptp) cc_final: 0.3005 (tpp) REVERT: E 813 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7870 (ttm110) REVERT: E 887 MET cc_start: 0.8130 (ptm) cc_final: 0.7751 (ppp) REVERT: F 745 MET cc_start: 0.8236 (tpp) cc_final: 0.7981 (tpp) REVERT: F 813 ARG cc_start: 0.8564 (ttp-110) cc_final: 0.8017 (tpt90) REVERT: F 909 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7058 (mp10) REVERT: F 970 GLN cc_start: 0.7154 (tm-30) cc_final: 0.6591 (tm-30) outliers start: 76 outliers final: 56 residues processed: 240 average time/residue: 0.3360 time to fit residues: 127.3340 Evaluate side-chains 224 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 165 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 918 HIS Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 709 HIS Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain E residue 652 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 879 HIS Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 927 SER Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 793 TYR Chi-restraints excluded: chain F residue 819 PHE Chi-restraints excluded: chain F residue 839 ASP Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 909 GLN Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 5.9990 chunk 222 optimal weight: 0.9990 chunk 237 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 186 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 214 optimal weight: 0.2980 chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 0.3980 chunk 155 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 667 ASN ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 571 ASN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 879 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22332 Z= 0.184 Angle : 0.563 11.678 30174 Z= 0.292 Chirality : 0.042 0.172 3312 Planarity : 0.004 0.069 3870 Dihedral : 4.533 19.317 2910 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.29 % Allowed : 18.93 % Favored : 78.78 % 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: 0.33 (0.17), residues: 2638 helix: 1.68 (0.16), residues: 1188 sheet: -0.00 (0.32), residues: 290 loop : -1.32 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 739 HIS 0.005 0.001 HIS B 53 PHE 0.021 0.001 PHE C 35 TYR 0.022 0.001 TYR D 815 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 187 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8974 (mmtp) cc_final: 0.8466 (mmmt) REVERT: A 24 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7568 (mp0) REVERT: A 25 LYS cc_start: 0.9221 (mptt) cc_final: 0.9013 (mmtp) REVERT: A 46 ARG cc_start: 0.8859 (ttp-110) cc_final: 0.8299 (tpt90) REVERT: A 54 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8419 (mm-40) REVERT: B 12 HIS cc_start: 0.7829 (t-90) cc_final: 0.7516 (t-90) REVERT: C 564 LYS cc_start: 0.8396 (ttpt) cc_final: 0.8172 (tmmt) REVERT: C 887 MET cc_start: 0.8430 (tmm) cc_final: 0.7908 (tmm) REVERT: C 957 GLN cc_start: 0.8472 (tp40) cc_final: 0.7627 (tp-100) REVERT: C 961 GLN cc_start: 0.8407 (mt0) cc_final: 0.8056 (mp10) REVERT: C 966 MET cc_start: 0.7922 (mpp) cc_final: 0.7310 (mpp) REVERT: D 709 HIS cc_start: 0.9109 (OUTLIER) cc_final: 0.8642 (m-70) REVERT: D 745 MET cc_start: 0.8572 (mmt) cc_final: 0.8150 (mmt) REVERT: E 141 MET cc_start: 0.0976 (mpp) cc_final: 0.0240 (ttp) REVERT: E 418 MET cc_start: 0.3378 (ptp) cc_final: 0.3020 (tpp) REVERT: E 813 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7960 (ttm110) REVERT: E 887 MET cc_start: 0.8441 (ptm) cc_final: 0.8103 (ppp) REVERT: F 813 ARG cc_start: 0.8570 (ttp-110) cc_final: 0.7944 (tpt90) REVERT: F 909 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7079 (mp10) REVERT: F 966 MET cc_start: 0.8216 (mtp) cc_final: 0.7383 (mpp) REVERT: F 970 GLN cc_start: 0.7224 (tm-30) cc_final: 0.6461 (tm-30) outliers start: 54 outliers final: 43 residues processed: 228 average time/residue: 0.3228 time to fit residues: 116.4064 Evaluate side-chains 220 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 175 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 889 SER Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 918 HIS Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain D residue 709 HIS Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain E residue 652 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 879 HIS Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 927 SER Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 793 TYR Chi-restraints excluded: chain F residue 819 PHE Chi-restraints excluded: chain F residue 839 ASP Chi-restraints excluded: chain F residue 909 GLN Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 HIS ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 482 GLN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 22332 Z= 0.345 Angle : 0.666 9.543 30174 Z= 0.349 Chirality : 0.046 0.185 3312 Planarity : 0.005 0.068 3870 Dihedral : 4.907 20.346 2910 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.63 % Allowed : 18.76 % Favored : 78.61 % 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: -0.08 (0.17), residues: 2638 helix: 1.28 (0.15), residues: 1188 sheet: -0.20 (0.31), residues: 290 loop : -1.45 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 486 HIS 0.009 0.001 HIS C 370 PHE 0.016 0.002 PHE C 35 TYR 0.027 0.002 TYR D 815 ARG 0.006 0.001 ARG C 931 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 167 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8973 (mmtp) cc_final: 0.8456 (mmmt) REVERT: A 24 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7573 (mp0) REVERT: A 49 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8097 (pp20) REVERT: A 54 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8478 (mm-40) REVERT: C 564 LYS cc_start: 0.8387 (ttpt) cc_final: 0.8109 (tmmt) REVERT: C 773 LYS cc_start: 0.6346 (mptt) cc_final: 0.5970 (ttmt) REVERT: C 887 MET cc_start: 0.8436 (tmm) cc_final: 0.7873 (tmm) REVERT: C 957 GLN cc_start: 0.8413 (tp40) cc_final: 0.8021 (tp-100) REVERT: C 961 GLN cc_start: 0.8483 (mt0) cc_final: 0.8032 (mt0) REVERT: C 966 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7369 (mpp) REVERT: D 709 HIS cc_start: 0.9220 (OUTLIER) cc_final: 0.8754 (m-70) REVERT: D 966 MET cc_start: 0.8462 (mtt) cc_final: 0.8245 (mtt) REVERT: E 141 MET cc_start: 0.1224 (mpp) cc_final: 0.0444 (ttm) REVERT: E 418 MET cc_start: 0.3187 (ptp) cc_final: 0.2802 (tpp) REVERT: E 813 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7946 (ttm110) REVERT: E 887 MET cc_start: 0.8110 (ptm) cc_final: 0.7847 (tmm) REVERT: F 813 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.7943 (tpt90) REVERT: F 909 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: F 966 MET cc_start: 0.8271 (mtp) cc_final: 0.7375 (mpp) REVERT: F 970 GLN cc_start: 0.7368 (tm-30) cc_final: 0.6629 (tm-30) outliers start: 62 outliers final: 47 residues processed: 216 average time/residue: 0.3301 time to fit residues: 113.0966 Evaluate side-chains 211 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 161 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 889 SER Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 918 HIS Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 709 HIS Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 455 GLU Chi-restraints excluded: chain E residue 652 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 879 HIS Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 927 SER Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 819 PHE Chi-restraints excluded: chain F residue 839 ASP Chi-restraints excluded: chain F residue 909 GLN Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 193 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.0670 chunk 209 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 184 optimal weight: 0.0270 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 83 ASN A 89 GLN C 86 HIS ** C 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 HIS ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.154984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.122614 restraints weight = 54161.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120631 restraints weight = 44014.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.121614 restraints weight = 33899.569| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22332 Z= 0.168 Angle : 0.568 8.365 30174 Z= 0.295 Chirality : 0.042 0.171 3312 Planarity : 0.004 0.069 3870 Dihedral : 4.466 19.273 2910 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.12 % Allowed : 19.27 % Favored : 78.61 % 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: 0.34 (0.17), residues: 2638 helix: 1.69 (0.16), residues: 1188 sheet: -0.04 (0.32), residues: 290 loop : -1.30 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 486 HIS 0.005 0.001 HIS B 53 PHE 0.021 0.001 PHE C 35 TYR 0.021 0.001 TYR D 815 ARG 0.004 0.000 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4002.85 seconds wall clock time: 74 minutes 21.50 seconds (4461.50 seconds total)