Starting phenix.real_space_refine on Wed Mar 20 23:57:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hy0_35084/03_2024/8hy0_35084_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hy0_35084/03_2024/8hy0_35084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hy0_35084/03_2024/8hy0_35084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hy0_35084/03_2024/8hy0_35084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hy0_35084/03_2024/8hy0_35084_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hy0_35084/03_2024/8hy0_35084_neut_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 340 5.49 5 S 102 5.16 5 C 17226 2.51 5 N 5098 2.21 5 O 6048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 812": "OE1" <-> "OE2" Residue "K GLU 878": "OE1" <-> "OE2" Residue "K GLU 1008": "OE1" <-> "OE2" Residue "K GLU 1160": "OE1" <-> "OE2" Residue "K GLU 1166": "OE1" <-> "OE2" Residue "L GLU 4": "OE1" <-> "OE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 118": "OE1" <-> "OE2" Residue "L GLU 129": "OE1" <-> "OE2" Residue "L GLU 260": "OE1" <-> "OE2" Residue "L GLU 289": "OE1" <-> "OE2" Residue "L GLU 342": "OE1" <-> "OE2" Residue "M GLU 262": "OE1" <-> "OE2" Residue "M GLU 280": "OE1" <-> "OE2" Residue "M GLU 302": "OE1" <-> "OE2" Residue "N GLU 178": "OE1" <-> "OE2" Residue "N GLU 359": "OE1" <-> "OE2" Residue "N GLU 571": "OE1" <-> "OE2" Residue "O GLU 262": "OE1" <-> "OE2" Residue "O GLU 268": "OE1" <-> "OE2" Residue "O GLU 280": "OE1" <-> "OE2" Residue "O GLU 302": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28821 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 837 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3466 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "J" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3504 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "K" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4597 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 12, 'TRANS': 536} Chain breaks: 2 Chain: "L" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3048 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 365} Chain: "M" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2398 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Chain: "N" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3073 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 4 Chain: "O" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1275 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "P" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1249 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23908 SG CYS N 263 75.494 93.776 92.040 1.00 58.89 S ATOM 23925 SG CYS N 266 74.616 91.077 89.480 1.00 62.13 S ATOM 24078 SG CYS N 286 77.192 93.761 88.551 1.00 45.24 S ATOM 23989 SG CYS N 275 76.508 103.330 99.753 1.00 85.58 S ATOM 24010 SG CYS N 278 72.529 103.314 99.284 1.00 90.86 S ATOM 24213 SG CYS N 303 74.840 104.681 96.637 1.00 88.55 S ATOM 24236 SG CYS N 306 74.443 106.489 99.878 1.00 98.42 S ATOM 25138 SG CYS N 417 61.690 54.244 67.578 1.00 30.71 S ATOM 25165 SG CYS N 420 61.658 50.519 66.769 1.00 35.54 S ATOM 25421 SG CYS N 451 64.910 52.529 66.471 1.00 46.29 S ATOM 25326 SG CYS N 440 60.466 66.139 69.617 1.00 42.65 S ATOM 25352 SG CYS N 443 57.546 65.738 67.010 1.00 20.36 S ATOM 25541 SG CYS N 466 61.077 64.437 66.076 1.00 59.47 S ATOM 27616 SG CYS P 263 29.608 108.959 29.751 1.00101.72 S ATOM 27633 SG CYS P 266 31.112 109.275 26.277 1.00108.72 S ATOM 27786 SG CYS P 286 29.713 105.852 27.160 1.00 95.81 S ATOM 27697 SG CYS P 275 24.784 106.389 41.257 1.00141.65 S ATOM 27718 SG CYS P 278 28.049 107.182 41.453 1.00142.16 S ATOM 27921 SG CYS P 303 27.780 103.591 40.423 1.00119.98 S ATOM 27944 SG CYS P 306 26.139 104.585 43.706 1.00139.05 S Time building chain proxies: 15.37, per 1000 atoms: 0.53 Number of scatterers: 28821 At special positions: 0 Unit cell: (139.65, 158.55, 199.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 102 16.00 P 340 15.00 O 6048 8.00 N 5098 7.00 C 17226 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: 13.27 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 501 " pdb="ZN ZN L 501 " - pdb=" ND1 HIS L 188 " pdb=" ZN N 701 " pdb="ZN ZN N 701 " - pdb=" ND1 HIS N 283 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 266 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 263 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 286 " pdb=" ZN N 702 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 303 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 306 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 278 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 275 " pdb=" ZN N 703 " pdb="ZN ZN N 703 " - pdb=" ND1 HIS N 448 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 417 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 451 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 420 " pdb=" ZN N 704 " pdb="ZN ZN N 704 " - pdb=" NE2 HIS N 469 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 443 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 466 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 440 " pdb=" ZN P 701 " pdb="ZN ZN P 701 " - pdb=" ND1 HIS P 283 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 266 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 263 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 286 " pdb=" ZN P 702 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 275 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 303 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 278 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 306 " Number of angles added : 24 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 9 sheets defined 50.9% alpha, 3.9% beta 168 base pairs and 299 stacking pairs defined. Time for finding SS restraints: 14.06 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 88 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 51 through 75 removed outlier: 3.523A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 45 through 71 removed outlier: 4.292A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 92 through 95 No H-bonds generated for 'chain 'C' and resid 92 through 95' Processing helix chain 'D' and resid 35 through 43 removed outlier: 3.504A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.534A pdb=" N ALA D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.518A pdb=" N VAL D 108 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER D 109 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 86 through 114 removed outlier: 4.204A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.512A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 51 through 75 removed outlier: 4.027A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 29 through 36 removed outlier: 3.644A pdb=" N LEU G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.065A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.631A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.826A pdb=" N HIS H 106 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER H 109 " --> pdb=" O HIS H 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 662 through 676 removed outlier: 5.208A pdb=" N PHE K 669 " --> pdb=" O GLU K 665 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU K 670 " --> pdb=" O VAL K 666 " (cutoff:3.500A) Processing helix chain 'K' and resid 679 through 693 Processing helix chain 'K' and resid 699 through 709 Processing helix chain 'K' and resid 714 through 724 Processing helix chain 'K' and resid 760 through 763 No H-bonds generated for 'chain 'K' and resid 760 through 763' Processing helix chain 'K' and resid 772 through 777 Processing helix chain 'K' and resid 786 through 789 No H-bonds generated for 'chain 'K' and resid 786 through 789' Processing helix chain 'K' and resid 802 through 839 Processing helix chain 'K' and resid 853 through 856 removed outlier: 4.311A pdb=" N GLY K 856 " --> pdb=" O PRO K 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 853 through 856' Processing helix chain 'K' and resid 862 through 870 Processing helix chain 'K' and resid 873 through 885 removed outlier: 4.344A pdb=" N PHE K 877 " --> pdb=" O LYS K 873 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU K 878 " --> pdb=" O GLU K 874 " (cutoff:3.500A) Processing helix chain 'K' and resid 887 through 927 Proline residue: K 892 - end of helix removed outlier: 3.759A pdb=" N VAL K 915 " --> pdb=" O GLU K 911 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE K 925 " --> pdb=" O GLN K 921 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS K 926 " --> pdb=" O LYS K 922 " (cutoff:3.500A) Processing helix chain 'K' and resid 935 through 942 Processing helix chain 'K' and resid 945 through 963 removed outlier: 3.637A pdb=" N ILE K 952 " --> pdb=" O LEU K 948 " (cutoff:3.500A) Processing helix chain 'K' and resid 983 through 998 Processing helix chain 'K' and resid 1004 through 1021 Processing helix chain 'K' and resid 1026 through 1032 Processing helix chain 'K' and resid 1142 through 1163 removed outlier: 3.534A pdb=" N ILE K1161 " --> pdb=" O ARG K1157 " (cutoff:3.500A) Processing helix chain 'K' and resid 1165 through 1173 Processing helix chain 'K' and resid 1179 through 1183 Processing helix chain 'K' and resid 1203 through 1216 Processing helix chain 'K' and resid 1221 through 1232 Processing helix chain 'K' and resid 1237 through 1239 No H-bonds generated for 'chain 'K' and resid 1237 through 1239' Processing helix chain 'K' and resid 1242 through 1257 Processing helix chain 'K' and resid 1263 through 1274 Processing helix chain 'K' and resid 1280 through 1293 removed outlier: 3.606A pdb=" N HIS K1293 " --> pdb=" O GLN K1289 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 42 through 54 removed outlier: 3.994A pdb=" N MET L 47 " --> pdb=" O ARG L 44 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER L 50 " --> pdb=" O MET L 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET L 53 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN L 54 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 60 Processing helix chain 'L' and resid 71 through 76 Processing helix chain 'L' and resid 80 through 88 Processing helix chain 'L' and resid 92 through 94 No H-bonds generated for 'chain 'L' and resid 92 through 94' Processing helix chain 'L' and resid 99 through 103 Processing helix chain 'L' and resid 116 through 135 Processing helix chain 'L' and resid 165 through 174 Processing helix chain 'L' and resid 191 through 196 Processing helix chain 'L' and resid 227 through 229 No H-bonds generated for 'chain 'L' and resid 227 through 229' Processing helix chain 'L' and resid 244 through 261 Proline residue: L 253 - end of helix Processing helix chain 'L' and resid 273 through 275 No H-bonds generated for 'chain 'L' and resid 273 through 275' Processing helix chain 'L' and resid 288 through 301 removed outlier: 4.115A pdb=" N CYS L 294 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL L 295 " --> pdb=" O HIS L 291 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE L 301 " --> pdb=" O TYR L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 330 removed outlier: 3.623A pdb=" N ASN L 330 " --> pdb=" O THR L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 344 through 346 No H-bonds generated for 'chain 'L' and resid 344 through 346' Processing helix chain 'L' and resid 366 through 382 removed outlier: 3.522A pdb=" N GLU L 381 " --> pdb=" O PHE L 377 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASN L 382 " --> pdb=" O ALA L 378 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 88 No H-bonds generated for 'chain 'M' and resid 86 through 88' Processing helix chain 'M' and resid 102 through 130 Processing helix chain 'M' and resid 226 through 240 Processing helix chain 'M' and resid 255 through 265 removed outlier: 3.645A pdb=" N GLU M 262 " --> pdb=" O LEU M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 296 removed outlier: 4.770A pdb=" N GLY M 294 " --> pdb=" O ASP M 290 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN M 295 " --> pdb=" O LYS M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 315 Processing helix chain 'M' and resid 328 through 343 Proline residue: M 339 - end of helix Processing helix chain 'M' and resid 349 through 368 removed outlier: 3.988A pdb=" N MET M 368 " --> pdb=" O VAL M 364 " (cutoff:3.500A) Processing helix chain 'M' and resid 370 through 373 No H-bonds generated for 'chain 'M' and resid 370 through 373' Processing helix chain 'M' and resid 392 through 400 Processing helix chain 'N' and resid 121 through 127 removed outlier: 4.696A pdb=" N GLU N 126 " --> pdb=" O LYS N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 175 No H-bonds generated for 'chain 'N' and resid 172 through 175' Processing helix chain 'N' and resid 304 through 314 Processing helix chain 'N' and resid 319 through 329 Processing helix chain 'N' and resid 337 through 342 Processing helix chain 'N' and resid 355 through 358 No H-bonds generated for 'chain 'N' and resid 355 through 358' Processing helix chain 'N' and resid 383 through 386 No H-bonds generated for 'chain 'N' and resid 383 through 386' Processing helix chain 'N' and resid 431 through 433 No H-bonds generated for 'chain 'N' and resid 431 through 433' Processing helix chain 'N' and resid 546 through 577 removed outlier: 3.745A pdb=" N PHE N 569 " --> pdb=" O LYS N 565 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU N 571 " --> pdb=" O PHE N 567 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER N 572 " --> pdb=" O GLN N 568 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU N 577 " --> pdb=" O LEU N 573 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 240 Processing helix chain 'O' and resid 254 through 268 removed outlier: 4.282A pdb=" N GLN O 267 " --> pdb=" O HIS O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 272 through 292 Processing helix chain 'O' and resid 303 through 313 Processing helix chain 'O' and resid 328 through 344 Proline residue: O 339 - end of helix removed outlier: 3.615A pdb=" N SER O 343 " --> pdb=" O PRO O 339 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER O 344 " --> pdb=" O GLU O 340 " (cutoff:3.500A) Processing helix chain 'O' and resid 350 through 368 Processing helix chain 'O' and resid 370 through 373 No H-bonds generated for 'chain 'O' and resid 370 through 373' Processing helix chain 'P' and resid 304 through 312 Processing helix chain 'P' and resid 316 through 329 Processing helix chain 'P' and resid 334 through 337 No H-bonds generated for 'chain 'P' and resid 334 through 337' Processing helix chain 'P' and resid 339 through 344 removed outlier: 3.905A pdb=" N ILE P 343 " --> pdb=" O LEU P 339 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP P 344 " --> pdb=" O LEU P 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 339 through 344' Processing helix chain 'P' and resid 355 through 358 No H-bonds generated for 'chain 'P' and resid 355 through 358' Processing helix chain 'P' and resid 544 through 579 Processing sheet with id= A, first strand: chain 'K' and resid 975 through 978 removed outlier: 3.703A pdb=" N HIS K1311 " --> pdb=" O ASP K1306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP K1306 " --> pdb=" O HIS K1311 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 62 through 64 removed outlier: 6.464A pdb=" N VAL L 141 " --> pdb=" O ALA L 22 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE L 24 " --> pdb=" O VAL L 141 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL L 143 " --> pdb=" O PHE L 24 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET L 305 " --> pdb=" O ALA L 142 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ASN L 144 " --> pdb=" O MET L 305 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL L 307 " --> pdb=" O ASN L 144 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 97 through 99 removed outlier: 6.564A pdb=" N PHE M 78 " --> pdb=" O LEU M 28 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'M' and resid 29 through 32 Processing sheet with id= E, first strand: chain 'M' and resid 244 through 246 Processing sheet with id= F, first strand: chain 'N' and resid 272 through 274 Processing sheet with id= G, first strand: chain 'N' and resid 437 through 439 Processing sheet with id= H, first strand: chain 'N' and resid 473 through 477 Processing sheet with id= I, first strand: chain 'N' and resid 85 through 87 removed outlier: 3.642A pdb=" N GLU N 86 " --> pdb=" O LYS N 95 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS N 95 " --> pdb=" O GLU N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id= I 949 hydrogen bonds defined for protein. 2715 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 429 hydrogen bonds 858 hydrogen bond angles 0 basepair planarities 168 basepair parallelities 299 stacking parallelities Total time for adding SS restraints: 18.57 Time building geometry restraints manager: 14.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4859 1.32 - 1.45: 9268 1.45 - 1.57: 15130 1.57 - 1.69: 680 1.69 - 1.81: 157 Bond restraints: 30094 Sorted by residual: bond pdb=" CA ARG L 44 " pdb=" C ARG L 44 " ideal model delta sigma weight residual 1.522 1.449 0.073 1.37e-02 5.33e+03 2.83e+01 bond pdb=" CA ARG D 96 " pdb=" C ARG D 96 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.29e-02 6.01e+03 2.24e+01 bond pdb=" CA LEU A 82 " pdb=" C LEU A 82 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.26e-02 6.30e+03 2.11e+01 bond pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 1.521 1.465 0.056 1.27e-02 6.20e+03 1.93e+01 bond pdb=" CA ALA D 107 " pdb=" C ALA D 107 " ideal model delta sigma weight residual 1.523 1.487 0.037 8.40e-03 1.42e+04 1.90e+01 ... (remaining 30089 not shown) Histogram of bond angle deviations from ideal: 96.06 - 104.08: 1343 104.08 - 112.10: 15678 112.10 - 120.12: 13001 120.12 - 128.14: 11477 128.14 - 136.16: 568 Bond angle restraints: 42067 Sorted by residual: angle pdb=" C ASN N 259 " pdb=" N GLU N 260 " pdb=" CA GLU N 260 " ideal model delta sigma weight residual 122.03 101.96 20.07 2.01e+00 2.48e-01 9.97e+01 angle pdb=" N ILE B 50 " pdb=" CA ILE B 50 " pdb=" C ILE B 50 " ideal model delta sigma weight residual 112.12 104.02 8.10 8.40e-01 1.42e+00 9.30e+01 angle pdb=" N GLU A 133 " pdb=" CA GLU A 133 " pdb=" C GLU A 133 " ideal model delta sigma weight residual 113.97 101.71 12.26 1.28e+00 6.10e-01 9.18e+01 angle pdb=" O ASN N 259 " pdb=" C ASN N 259 " pdb=" N GLU N 260 " ideal model delta sigma weight residual 122.23 134.15 -11.92 1.33e+00 5.65e-01 8.04e+01 angle pdb=" CA ASN N 259 " pdb=" C ASN N 259 " pdb=" N GLU N 260 " ideal model delta sigma weight residual 115.82 102.63 13.19 1.60e+00 3.91e-01 6.80e+01 ... (remaining 42062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 15403 35.95 - 71.89: 1872 71.89 - 107.84: 22 107.84 - 143.79: 1 143.79 - 179.73: 4 Dihedral angle restraints: 17302 sinusoidal: 9403 harmonic: 7899 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual 180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA VAL K 923 " pdb=" C VAL K 923 " pdb=" N PHE K 924 " pdb=" CA PHE K 924 " ideal model delta harmonic sigma weight residual -180.00 -157.78 -22.22 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 17299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3769 0.055 - 0.111: 750 0.111 - 0.166: 114 0.166 - 0.222: 14 0.222 - 0.277: 6 Chirality restraints: 4653 Sorted by residual: chirality pdb=" CB VAL O 337 " pdb=" CA VAL O 337 " pdb=" CG1 VAL O 337 " pdb=" CG2 VAL O 337 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB VAL L 363 " pdb=" CA VAL L 363 " pdb=" CG1 VAL L 363 " pdb=" CG2 VAL L 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR D 112 " pdb=" CA THR D 112 " pdb=" OG1 THR D 112 " pdb=" CG2 THR D 112 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 4650 not shown) Planarity restraints: 4165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU N 507 " 0.102 5.00e-02 4.00e+02 1.49e-01 3.55e+01 pdb=" N PRO N 508 " -0.257 5.00e-02 4.00e+02 pdb=" CA PRO N 508 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO N 508 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 101 " -0.026 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" C VAL A 101 " 0.090 2.00e-02 2.50e+03 pdb=" O VAL A 101 " -0.033 2.00e-02 2.50e+03 pdb=" N ALA A 102 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 72 " -0.024 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C ARG A 72 " 0.088 2.00e-02 2.50e+03 pdb=" O ARG A 72 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU A 73 " -0.030 2.00e-02 2.50e+03 ... (remaining 4162 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 780 2.65 - 3.21: 25786 3.21 - 3.78: 52400 3.78 - 4.34: 69205 4.34 - 4.90: 101957 Nonbonded interactions: 250128 Sorted by model distance: nonbonded pdb=" OD1 ASP L 186 " pdb="ZN ZN L 501 " model vdw 2.090 2.230 nonbonded pdb=" OD2 ASP L 274 " pdb="ZN ZN L 501 " model vdw 2.208 2.230 nonbonded pdb=" O ASN K 663 " pdb=" OG1 THR K 667 " model vdw 2.209 2.440 nonbonded pdb=" NH2 ARG B 35 " pdb=" OH TYR B 51 " model vdw 2.220 2.520 nonbonded pdb=" O ARG K1308 " pdb=" OG1 THR K1309 " model vdw 2.260 2.440 ... (remaining 250123 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' and (resid 33 through 34 or resid 37 through 134)) selection = (chain 'E' and (resid 12 through 13 or resid 18 or resid 38 through 134)) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = (chain 'H' and resid 29 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.270 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 98.480 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 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 : 0.007 0.079 30094 Z= 0.422 Angle : 0.960 20.074 42067 Z= 0.605 Chirality : 0.047 0.277 4653 Planarity : 0.007 0.149 4165 Dihedral : 23.110 179.735 12190 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 16.83 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -1.87 (0.15), residues: 2640 helix: -1.16 (0.12), residues: 1420 sheet: -0.37 (0.47), residues: 122 loop : -1.26 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K1223 HIS 0.008 0.001 HIS N 469 PHE 0.039 0.002 PHE N 311 TYR 0.033 0.002 TYR A 99 ARG 0.012 0.001 ARG N 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 620 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.7157 (tttt) cc_final: 0.6952 (ttpp) REVERT: B 79 LYS cc_start: 0.7371 (mmmm) cc_final: 0.6911 (mmtp) REVERT: C 41 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7807 (mp0) REVERT: C 73 ASN cc_start: 0.8402 (t0) cc_final: 0.8047 (t0) REVERT: C 92 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7868 (mp0) REVERT: D 46 HIS cc_start: 0.6425 (m-70) cc_final: 0.5835 (m90) REVERT: D 47 PRO cc_start: 0.8473 (Cg_exo) cc_final: 0.7952 (Cg_endo) REVERT: D 81 ASN cc_start: 0.8716 (m110) cc_final: 0.8270 (m110) REVERT: E 52 ARG cc_start: 0.7455 (mtt90) cc_final: 0.7073 (mtm-85) REVERT: E 94 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7534 (mm-30) REVERT: F 27 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7037 (tp-100) REVERT: F 77 LYS cc_start: 0.8470 (mttt) cc_final: 0.8246 (mttm) REVERT: F 79 LYS cc_start: 0.7558 (mttp) cc_final: 0.7236 (mtpp) REVERT: G 36 LYS cc_start: 0.8660 (mttt) cc_final: 0.8272 (mttm) REVERT: G 38 ASN cc_start: 0.8187 (m-40) cc_final: 0.7542 (m-40) REVERT: G 84 GLN cc_start: 0.7695 (tp40) cc_final: 0.7438 (tp40) REVERT: H 65 ASP cc_start: 0.7630 (t0) cc_final: 0.7184 (t0) REVERT: H 82 LYS cc_start: 0.8243 (mttt) cc_final: 0.8039 (mmmt) REVERT: H 84 SER cc_start: 0.7296 (m) cc_final: 0.6459 (p) REVERT: H 90 GLU cc_start: 0.7501 (mp0) cc_final: 0.6543 (mp0) REVERT: K 721 LYS cc_start: 0.7541 (ttpt) cc_final: 0.7220 (tptp) REVERT: K 885 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6579 (mm-30) REVERT: K 904 GLU cc_start: 0.7540 (tt0) cc_final: 0.7091 (tt0) REVERT: K 982 LYS cc_start: 0.7849 (mttt) cc_final: 0.7429 (mmtp) REVERT: K 990 CYS cc_start: 0.7972 (t) cc_final: 0.7436 (t) REVERT: K 1015 LYS cc_start: 0.7101 (mttt) cc_final: 0.6815 (mttm) REVERT: K 1136 PHE cc_start: 0.7997 (m-80) cc_final: 0.7686 (m-80) REVERT: K 1166 GLU cc_start: 0.7627 (pp20) cc_final: 0.7194 (pm20) REVERT: K 1205 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7370 (mttm) REVERT: K 1209 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7384 (ttp-110) REVERT: K 1244 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7187 (mmtm) REVERT: K 1271 LYS cc_start: 0.7976 (mttt) cc_final: 0.7533 (mttp) REVERT: L 28 ASP cc_start: 0.8461 (m-30) cc_final: 0.8239 (m-30) REVERT: L 67 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8101 (ttpp) REVERT: L 95 GLU cc_start: 0.7384 (pm20) cc_final: 0.7107 (pm20) REVERT: L 96 MET cc_start: 0.7474 (ttp) cc_final: 0.6874 (mpp) REVERT: L 98 LYS cc_start: 0.7196 (ptmt) cc_final: 0.6955 (tppt) REVERT: L 220 GLU cc_start: 0.8029 (tp30) cc_final: 0.7769 (tp30) REVERT: L 230 LYS cc_start: 0.8661 (tttm) cc_final: 0.8371 (tttp) REVERT: L 305 MET cc_start: 0.9208 (ptp) cc_final: 0.8863 (ptm) REVERT: L 335 ASP cc_start: 0.7571 (p0) cc_final: 0.6758 (t70) REVERT: M 107 MET cc_start: 0.6546 (ppp) cc_final: 0.6119 (ppp) REVERT: M 111 LEU cc_start: 0.9052 (mt) cc_final: 0.8721 (mt) REVERT: M 275 GLN cc_start: 0.6809 (mm-40) cc_final: 0.6558 (mm110) REVERT: M 353 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6721 (mt0) REVERT: M 357 LYS cc_start: 0.7254 (tmtt) cc_final: 0.6744 (tptt) REVERT: N 121 GLU cc_start: 0.7135 (mp0) cc_final: 0.6564 (mt-10) REVERT: N 267 ASN cc_start: 0.8186 (m110) cc_final: 0.7952 (m-40) REVERT: N 305 GLU cc_start: 0.7072 (tt0) cc_final: 0.6707 (mt-10) REVERT: N 352 GLN cc_start: 0.8180 (mm110) cc_final: 0.7906 (tt0) REVERT: N 375 GLU cc_start: 0.7640 (pt0) cc_final: 0.7300 (pm20) REVERT: N 393 GLN cc_start: 0.7515 (mt0) cc_final: 0.7194 (mt0) REVERT: N 413 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7241 (mmtm) REVERT: N 511 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7943 (mtpt) REVERT: N 560 MET cc_start: 0.7365 (mmm) cc_final: 0.7142 (mmm) REVERT: O 256 MET cc_start: 0.6736 (mmm) cc_final: 0.6530 (mmm) REVERT: O 278 LEU cc_start: 0.8204 (tp) cc_final: 0.7964 (tp) REVERT: P 320 LYS cc_start: 0.8376 (mttt) cc_final: 0.7953 (mtmt) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.4598 time to fit residues: 426.6052 Evaluate side-chains 485 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 151 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 232 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 68 ASN C 73 ASN C 112 GLN D 46 HIS D 92 GLN E 19 GLN E 68 GLN E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN K 690 ASN K 694 GLN ** K 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 937 GLN K1150 HIS K1190 GLN L 362 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 393 GLN N 502 ASN N 517 ASN O 275 GLN ** O 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 30094 Z= 0.325 Angle : 0.608 12.100 42067 Z= 0.339 Chirality : 0.040 0.199 4653 Planarity : 0.005 0.085 4165 Dihedral : 26.311 176.767 6658 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.42 % Allowed : 18.58 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.43 (0.16), residues: 2640 helix: 0.27 (0.13), residues: 1457 sheet: -0.66 (0.45), residues: 129 loop : -0.91 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K1151 HIS 0.006 0.001 HIS P 283 PHE 0.018 0.002 PHE H 67 TYR 0.031 0.002 TYR H 80 ARG 0.007 0.001 ARG M 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 531 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8677 (tp) cc_final: 0.8307 (tp) REVERT: A 81 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8171 (p0) REVERT: A 86 SER cc_start: 0.9049 (p) cc_final: 0.8699 (t) REVERT: B 31 LYS cc_start: 0.7306 (tttt) cc_final: 0.6906 (tttm) REVERT: C 41 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7819 (mp0) REVERT: C 73 ASN cc_start: 0.8402 (t0) cc_final: 0.7917 (t0) REVERT: C 91 GLU cc_start: 0.8095 (tt0) cc_final: 0.7875 (tm-30) REVERT: C 92 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7307 (mm-30) REVERT: C 99 ARG cc_start: 0.7449 (ptp-110) cc_final: 0.7249 (mtp85) REVERT: C 116 LEU cc_start: 0.7344 (mm) cc_final: 0.6979 (mm) REVERT: D 46 HIS cc_start: 0.6907 (m90) cc_final: 0.6205 (m170) REVERT: D 65 ASP cc_start: 0.8732 (t0) cc_final: 0.8315 (t0) REVERT: D 81 ASN cc_start: 0.9127 (m110) cc_final: 0.8847 (m110) REVERT: D 90 GLU cc_start: 0.6956 (tt0) cc_final: 0.6732 (tt0) REVERT: E 60 LEU cc_start: 0.7923 (mt) cc_final: 0.7689 (mt) REVERT: E 79 LYS cc_start: 0.7732 (tttp) cc_final: 0.7342 (tttp) REVERT: E 94 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7723 (mm-30) REVERT: F 27 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7653 (tp40) REVERT: F 74 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: F 77 LYS cc_start: 0.8745 (mttt) cc_final: 0.8157 (mmmt) REVERT: F 79 LYS cc_start: 0.7770 (mttp) cc_final: 0.7399 (mmtm) REVERT: G 36 LYS cc_start: 0.8774 (mttt) cc_final: 0.8518 (mttm) REVERT: G 38 ASN cc_start: 0.8161 (m-40) cc_final: 0.7522 (m-40) REVERT: G 90 ASP cc_start: 0.6584 (t0) cc_final: 0.6341 (t0) REVERT: G 104 GLN cc_start: 0.7385 (mp10) cc_final: 0.7078 (mp10) REVERT: H 32 GLU cc_start: 0.7441 (pt0) cc_final: 0.6832 (pt0) REVERT: H 39 TYR cc_start: 0.6148 (t80) cc_final: 0.5943 (t80) REVERT: H 52 SER cc_start: 0.8254 (t) cc_final: 0.7703 (p) REVERT: H 60 ASN cc_start: 0.6949 (t0) cc_final: 0.6717 (t0) REVERT: H 65 ASP cc_start: 0.7672 (t0) cc_final: 0.7451 (t0) REVERT: H 82 LYS cc_start: 0.8641 (mttt) cc_final: 0.8293 (mmmt) REVERT: K 707 ASP cc_start: 0.7955 (t0) cc_final: 0.7449 (t0) REVERT: K 764 PHE cc_start: 0.7336 (m-10) cc_final: 0.7068 (m-10) REVERT: K 850 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7784 (mtpt) REVERT: K 860 MET cc_start: 0.7275 (mmm) cc_final: 0.6581 (mmt) REVERT: K 871 TYR cc_start: 0.8089 (m-80) cc_final: 0.7863 (m-80) REVERT: K 904 GLU cc_start: 0.7590 (tt0) cc_final: 0.7032 (tt0) REVERT: K 928 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8780 (mp) REVERT: K 982 LYS cc_start: 0.7811 (mttt) cc_final: 0.7356 (mtpt) REVERT: K 983 ASN cc_start: 0.7623 (m-40) cc_final: 0.7345 (m110) REVERT: K 1008 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6545 (mt-10) REVERT: K 1015 LYS cc_start: 0.7369 (mttt) cc_final: 0.6837 (mptp) REVERT: K 1166 GLU cc_start: 0.7707 (pp20) cc_final: 0.7272 (pm20) REVERT: K 1167 ARG cc_start: 0.7231 (ttp80) cc_final: 0.7015 (ttp-110) REVERT: K 1182 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7361 (tppt) REVERT: K 1187 LEU cc_start: 0.8486 (mt) cc_final: 0.8206 (mt) REVERT: K 1194 MET cc_start: 0.8286 (mtp) cc_final: 0.7922 (mtt) REVERT: K 1205 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7484 (mttm) REVERT: K 1244 LYS cc_start: 0.7505 (mmtt) cc_final: 0.7197 (mmtm) REVERT: K 1266 MET cc_start: 0.7990 (mmm) cc_final: 0.7663 (mmp) REVERT: K 1271 LYS cc_start: 0.8054 (mttt) cc_final: 0.7588 (ttpp) REVERT: K 1285 ILE cc_start: 0.8742 (tp) cc_final: 0.8541 (tp) REVERT: K 1287 ARG cc_start: 0.7149 (ttm-80) cc_final: 0.6888 (ttp80) REVERT: K 1298 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7210 (mt-10) REVERT: K 1310 LEU cc_start: 0.8550 (mp) cc_final: 0.8240 (mt) REVERT: L 61 MET cc_start: 0.9170 (ptp) cc_final: 0.8920 (ptp) REVERT: L 88 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7786 (mtm-85) REVERT: L 95 GLU cc_start: 0.7509 (pm20) cc_final: 0.7279 (pm20) REVERT: L 96 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7088 (mtp) REVERT: L 98 LYS cc_start: 0.7569 (ptmt) cc_final: 0.7212 (tppt) REVERT: L 230 LYS cc_start: 0.8596 (tttm) cc_final: 0.8324 (tttp) REVERT: L 289 GLU cc_start: 0.8139 (mp0) cc_final: 0.7678 (mp0) REVERT: L 335 ASP cc_start: 0.7543 (p0) cc_final: 0.6878 (t70) REVERT: L 363 VAL cc_start: 0.8616 (p) cc_final: 0.8249 (m) REVERT: M 255 GLU cc_start: 0.7799 (tt0) cc_final: 0.7487 (tt0) REVERT: M 256 MET cc_start: 0.7966 (mtp) cc_final: 0.7649 (mtp) REVERT: M 275 GLN cc_start: 0.6843 (mm-40) cc_final: 0.6632 (mm110) REVERT: M 308 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7209 (mm-30) REVERT: M 353 GLN cc_start: 0.7287 (mm-40) cc_final: 0.6804 (mt0) REVERT: M 357 LYS cc_start: 0.7424 (tmtt) cc_final: 0.6936 (ttpt) REVERT: M 395 GLU cc_start: 0.8185 (tt0) cc_final: 0.7804 (tt0) REVERT: N 116 ASN cc_start: 0.7447 (m-40) cc_final: 0.6864 (t0) REVERT: N 121 GLU cc_start: 0.7113 (mp0) cc_final: 0.6604 (mt-10) REVERT: N 260 GLU cc_start: 0.7337 (mp0) cc_final: 0.6470 (mp0) REVERT: N 267 ASN cc_start: 0.8236 (m110) cc_final: 0.8010 (m-40) REVERT: N 292 ASP cc_start: 0.7476 (t70) cc_final: 0.7252 (t70) REVERT: N 305 GLU cc_start: 0.7038 (tt0) cc_final: 0.6729 (mt-10) REVERT: N 342 ASN cc_start: 0.7337 (m-40) cc_final: 0.6527 (t0) REVERT: N 352 GLN cc_start: 0.8403 (mm110) cc_final: 0.8087 (tt0) REVERT: N 375 GLU cc_start: 0.7823 (pt0) cc_final: 0.7348 (pm20) REVERT: N 393 GLN cc_start: 0.7344 (mt0) cc_final: 0.7130 (mt0) REVERT: N 413 LYS cc_start: 0.8352 (mtmt) cc_final: 0.8138 (mtpp) REVERT: N 500 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7908 (mmmt) REVERT: N 511 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7726 (mtmm) REVERT: N 512 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8509 (mm) REVERT: N 515 GLN cc_start: 0.7703 (mt0) cc_final: 0.7201 (mm-40) REVERT: O 311 LYS cc_start: 0.8266 (mtmm) cc_final: 0.7738 (mppt) REVERT: P 320 LYS cc_start: 0.8466 (mttt) cc_final: 0.8051 (mtmt) outliers start: 82 outliers final: 37 residues processed: 579 average time/residue: 0.4482 time to fit residues: 396.7206 Evaluate side-chains 535 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 493 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1189 SER Chi-restraints excluded: chain K residue 1192 SER Chi-restraints excluded: chain K residue 1199 VAL Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 392 SER Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 360 THR Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 223 optimal weight: 0.0270 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 60.0000 chunk 269 optimal weight: 0.0670 chunk 290 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 91 optimal weight: 60.0000 chunk 216 optimal weight: 1.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS G 31 HIS H 46 HIS H 81 ASN K 694 GLN K 930 HIS L 72 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 410 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30094 Z= 0.298 Angle : 0.568 8.862 42067 Z= 0.320 Chirality : 0.039 0.170 4653 Planarity : 0.005 0.061 4165 Dihedral : 26.238 178.870 6658 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.42 % Allowed : 18.70 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.12 (0.16), residues: 2640 helix: 0.80 (0.14), residues: 1466 sheet: -0.69 (0.46), residues: 118 loop : -0.76 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K1151 HIS 0.011 0.001 HIS P 283 PHE 0.023 0.002 PHE M 17 TYR 0.024 0.002 TYR H 80 ARG 0.007 0.000 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 510 time to evaluate : 2.707 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 74 ILE cc_start: 0.8566 (tp) cc_final: 0.8228 (tp) REVERT: A 129 ARG cc_start: 0.7469 (tpt-90) cc_final: 0.7173 (tpt90) REVERT: B 31 LYS cc_start: 0.7262 (tttt) cc_final: 0.6915 (tttm) REVERT: B 82 THR cc_start: 0.8064 (m) cc_final: 0.7832 (m) REVERT: C 36 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8135 (mtpt) REVERT: C 41 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7754 (mp0) REVERT: C 64 GLU cc_start: 0.7546 (tt0) cc_final: 0.6806 (tp30) REVERT: C 73 ASN cc_start: 0.8341 (t0) cc_final: 0.7891 (t0) REVERT: C 91 GLU cc_start: 0.8081 (tt0) cc_final: 0.7717 (tm-30) REVERT: C 116 LEU cc_start: 0.7349 (mm) cc_final: 0.6939 (mm) REVERT: D 39 TYR cc_start: 0.7687 (t80) cc_final: 0.7326 (t80) REVERT: D 46 HIS cc_start: 0.6953 (m-70) cc_final: 0.6161 (m170) REVERT: D 65 ASP cc_start: 0.8691 (t0) cc_final: 0.8380 (t0) REVERT: D 81 ASN cc_start: 0.9066 (m110) cc_final: 0.8712 (m110) REVERT: D 90 GLU cc_start: 0.7101 (tt0) cc_final: 0.6792 (tt0) REVERT: E 94 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7782 (mm-30) REVERT: F 44 LYS cc_start: 0.8462 (tttm) cc_final: 0.8126 (tttp) REVERT: F 77 LYS cc_start: 0.8554 (mttt) cc_final: 0.8002 (mmmt) REVERT: F 79 LYS cc_start: 0.7649 (mttp) cc_final: 0.7294 (mmtm) REVERT: G 36 LYS cc_start: 0.8684 (mttt) cc_final: 0.8454 (mttm) REVERT: G 38 ASN cc_start: 0.7958 (m-40) cc_final: 0.7539 (m-40) REVERT: G 84 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7610 (tp-100) REVERT: G 90 ASP cc_start: 0.6609 (t0) cc_final: 0.6352 (t0) REVERT: G 104 GLN cc_start: 0.7572 (mp10) cc_final: 0.7283 (mp10) REVERT: H 39 TYR cc_start: 0.6082 (t80) cc_final: 0.5756 (t80) REVERT: H 52 SER cc_start: 0.8438 (t) cc_final: 0.8026 (p) REVERT: H 65 ASP cc_start: 0.7739 (t0) cc_final: 0.7439 (t0) REVERT: K 670 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: K 707 ASP cc_start: 0.7997 (t0) cc_final: 0.7445 (t0) REVERT: K 764 PHE cc_start: 0.7364 (m-10) cc_final: 0.7084 (m-10) REVERT: K 850 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7883 (mtpt) REVERT: K 860 MET cc_start: 0.7349 (mmm) cc_final: 0.6744 (mmt) REVERT: K 982 LYS cc_start: 0.7879 (mttt) cc_final: 0.7314 (mtpt) REVERT: K 986 TYR cc_start: 0.7781 (m-10) cc_final: 0.7479 (m-80) REVERT: K 1008 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6586 (mt-10) REVERT: K 1015 LYS cc_start: 0.7311 (mttt) cc_final: 0.6835 (mptp) REVERT: K 1155 TYR cc_start: 0.9003 (t80) cc_final: 0.8793 (t80) REVERT: K 1166 GLU cc_start: 0.7696 (pp20) cc_final: 0.7264 (pm20) REVERT: K 1182 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7382 (tppt) REVERT: K 1194 MET cc_start: 0.8215 (mtp) cc_final: 0.7799 (mtt) REVERT: K 1205 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7453 (mttm) REVERT: K 1244 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7192 (mmtm) REVERT: K 1266 MET cc_start: 0.7996 (mmm) cc_final: 0.7637 (tpt) REVERT: K 1271 LYS cc_start: 0.7900 (mttt) cc_final: 0.7360 (ttmm) REVERT: K 1272 ASP cc_start: 0.7927 (t0) cc_final: 0.7610 (t70) REVERT: K 1285 ILE cc_start: 0.8707 (tp) cc_final: 0.8446 (tp) REVERT: K 1287 ARG cc_start: 0.7329 (ttm-80) cc_final: 0.7037 (ttp80) REVERT: K 1310 LEU cc_start: 0.8493 (mp) cc_final: 0.8170 (mt) REVERT: L 53 MET cc_start: 0.9016 (mmp) cc_final: 0.8781 (mmp) REVERT: L 60 LYS cc_start: 0.8014 (mttm) cc_final: 0.7278 (mttt) REVERT: L 61 MET cc_start: 0.9114 (ptp) cc_final: 0.8824 (ptp) REVERT: L 96 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7111 (mtp) REVERT: L 98 LYS cc_start: 0.7602 (ptmt) cc_final: 0.7192 (tppt) REVERT: L 230 LYS cc_start: 0.8550 (tttm) cc_final: 0.8255 (tttp) REVERT: L 289 GLU cc_start: 0.8086 (mp0) cc_final: 0.7883 (mp0) REVERT: L 335 ASP cc_start: 0.7602 (p0) cc_final: 0.6903 (t70) REVERT: L 363 VAL cc_start: 0.8587 (p) cc_final: 0.8342 (m) REVERT: M 260 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7566 (ttpp) REVERT: M 308 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7149 (mm-30) REVERT: M 353 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6771 (mt0) REVERT: M 357 LYS cc_start: 0.7493 (tmtt) cc_final: 0.7003 (tttp) REVERT: M 373 TYR cc_start: 0.8861 (m-80) cc_final: 0.8550 (m-80) REVERT: N 121 GLU cc_start: 0.6974 (mp0) cc_final: 0.6523 (mt-10) REVERT: N 267 ASN cc_start: 0.8271 (m110) cc_final: 0.8067 (m-40) REVERT: N 292 ASP cc_start: 0.7492 (t70) cc_final: 0.7129 (t70) REVERT: N 295 ASN cc_start: 0.8110 (t0) cc_final: 0.7459 (m110) REVERT: N 305 GLU cc_start: 0.7079 (tt0) cc_final: 0.6645 (mt-10) REVERT: N 342 ASN cc_start: 0.7517 (m-40) cc_final: 0.6705 (t0) REVERT: N 375 GLU cc_start: 0.7844 (pt0) cc_final: 0.7359 (pm20) REVERT: N 402 ASN cc_start: 0.8328 (m-40) cc_final: 0.8039 (m-40) REVERT: N 413 LYS cc_start: 0.8305 (mtmt) cc_final: 0.8095 (mtpp) REVERT: N 512 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8492 (mm) REVERT: N 515 GLN cc_start: 0.7681 (mt0) cc_final: 0.7175 (mm-40) REVERT: O 311 LYS cc_start: 0.8270 (mtmm) cc_final: 0.8038 (mtmm) REVERT: P 554 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7073 (tttm) outliers start: 82 outliers final: 58 residues processed: 558 average time/residue: 0.4484 time to fit residues: 378.6521 Evaluate side-chains 547 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 484 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1189 SER Chi-restraints excluded: chain K residue 1192 SER Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 260 LYS Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain N residue 360 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 348 ASP Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 0.0870 chunk 202 optimal weight: 30.0000 chunk 139 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 180 optimal weight: 0.3980 chunk 270 optimal weight: 9.9990 chunk 286 optimal weight: 20.0000 chunk 141 optimal weight: 0.7980 chunk 256 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 104 GLN E 39 HIS E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 389 ASN N 393 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30094 Z= 0.195 Angle : 0.521 7.848 42067 Z= 0.296 Chirality : 0.036 0.169 4653 Planarity : 0.004 0.050 4165 Dihedral : 26.022 178.412 6658 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.29 % Allowed : 19.78 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2640 helix: 1.17 (0.14), residues: 1464 sheet: -0.71 (0.45), residues: 118 loop : -0.62 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 31 HIS 0.006 0.001 HIS E 39 PHE 0.027 0.001 PHE M 17 TYR 0.019 0.001 TYR L 313 ARG 0.007 0.000 ARG M 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 491 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8595 (tp) cc_final: 0.8295 (tp) REVERT: A 94 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: A 129 ARG cc_start: 0.7368 (tpt-90) cc_final: 0.7160 (tpt90) REVERT: B 31 LYS cc_start: 0.7270 (tttt) cc_final: 0.6875 (tttm) REVERT: C 36 LYS cc_start: 0.8373 (mtmm) cc_final: 0.8086 (mtpt) REVERT: C 41 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7667 (mp0) REVERT: C 64 GLU cc_start: 0.7543 (tt0) cc_final: 0.6945 (tp30) REVERT: C 73 ASN cc_start: 0.8352 (t0) cc_final: 0.7906 (t0) REVERT: C 91 GLU cc_start: 0.8060 (tt0) cc_final: 0.7698 (tm-30) REVERT: C 116 LEU cc_start: 0.7396 (mm) cc_final: 0.6961 (mm) REVERT: D 39 TYR cc_start: 0.7690 (t80) cc_final: 0.7345 (t80) REVERT: D 46 HIS cc_start: 0.7071 (m-70) cc_final: 0.6512 (m-70) REVERT: D 65 ASP cc_start: 0.8656 (t0) cc_final: 0.8309 (t0) REVERT: D 81 ASN cc_start: 0.9064 (m110) cc_final: 0.8795 (m110) REVERT: D 82 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8844 (mmmt) REVERT: D 90 GLU cc_start: 0.7068 (tt0) cc_final: 0.6862 (tt0) REVERT: F 77 LYS cc_start: 0.8437 (mttt) cc_final: 0.7931 (mmmt) REVERT: F 79 LYS cc_start: 0.7688 (mttp) cc_final: 0.7331 (mmtm) REVERT: G 38 ASN cc_start: 0.7933 (m-40) cc_final: 0.7514 (m-40) REVERT: G 84 GLN cc_start: 0.8066 (tp-100) cc_final: 0.7753 (tp-100) REVERT: G 90 ASP cc_start: 0.6481 (t0) cc_final: 0.6243 (t0) REVERT: H 39 TYR cc_start: 0.6490 (t80) cc_final: 0.6273 (t80) REVERT: H 52 SER cc_start: 0.8404 (t) cc_final: 0.8047 (p) REVERT: H 61 SER cc_start: 0.7814 (t) cc_final: 0.7257 (m) REVERT: H 65 ASP cc_start: 0.7735 (t0) cc_final: 0.7464 (t0) REVERT: K 670 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: K 764 PHE cc_start: 0.7338 (m-10) cc_final: 0.7057 (m-10) REVERT: K 860 MET cc_start: 0.7306 (mmm) cc_final: 0.6688 (mmt) REVERT: K 982 LYS cc_start: 0.7858 (mttt) cc_final: 0.7289 (mtpt) REVERT: K 986 TYR cc_start: 0.7820 (m-10) cc_final: 0.7451 (m-80) REVERT: K 1008 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6575 (mt-10) REVERT: K 1015 LYS cc_start: 0.7299 (mttt) cc_final: 0.6829 (mptp) REVERT: K 1155 TYR cc_start: 0.8943 (t80) cc_final: 0.8741 (t80) REVERT: K 1166 GLU cc_start: 0.7751 (pp20) cc_final: 0.7312 (pm20) REVERT: K 1167 ARG cc_start: 0.7275 (ttp80) cc_final: 0.7061 (ttp80) REVERT: K 1182 LYS cc_start: 0.7557 (mmtt) cc_final: 0.7337 (tppt) REVERT: K 1194 MET cc_start: 0.8224 (mtp) cc_final: 0.7814 (mtt) REVERT: K 1205 LYS cc_start: 0.7765 (mmtt) cc_final: 0.7485 (mttm) REVERT: K 1244 LYS cc_start: 0.7450 (mmtt) cc_final: 0.7238 (mmtm) REVERT: K 1266 MET cc_start: 0.7971 (mmm) cc_final: 0.7696 (mmp) REVERT: K 1271 LYS cc_start: 0.7920 (mttt) cc_final: 0.7414 (ttmm) REVERT: K 1272 ASP cc_start: 0.7868 (t0) cc_final: 0.7576 (t70) REVERT: K 1285 ILE cc_start: 0.8758 (tp) cc_final: 0.8465 (tp) REVERT: K 1287 ARG cc_start: 0.7263 (ttm-80) cc_final: 0.6996 (ttp80) REVERT: L 53 MET cc_start: 0.9021 (mmp) cc_final: 0.8807 (mmp) REVERT: L 60 LYS cc_start: 0.8073 (mttm) cc_final: 0.7319 (mttt) REVERT: L 61 MET cc_start: 0.8977 (ptp) cc_final: 0.8656 (ptp) REVERT: L 96 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7147 (mtp) REVERT: L 98 LYS cc_start: 0.7562 (ptmt) cc_final: 0.7159 (tppt) REVERT: L 114 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6553 (p0) REVERT: L 205 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8875 (m) REVERT: L 230 LYS cc_start: 0.8548 (tttm) cc_final: 0.8293 (tttp) REVERT: L 289 GLU cc_start: 0.8216 (mp0) cc_final: 0.7915 (mp0) REVERT: L 335 ASP cc_start: 0.7585 (p0) cc_final: 0.6817 (t70) REVERT: L 336 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6862 (mttp) REVERT: L 363 VAL cc_start: 0.8650 (p) cc_final: 0.8209 (m) REVERT: M 111 LEU cc_start: 0.8751 (mt) cc_final: 0.8383 (mt) REVERT: M 260 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7312 (ttpp) REVERT: M 308 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7079 (mm-30) REVERT: M 353 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6714 (mt0) REVERT: M 357 LYS cc_start: 0.7489 (tmtt) cc_final: 0.6992 (tttp) REVERT: N 121 GLU cc_start: 0.7042 (mp0) cc_final: 0.6580 (mt-10) REVERT: N 175 MET cc_start: 0.7026 (mtt) cc_final: 0.6704 (ptp) REVERT: N 267 ASN cc_start: 0.8264 (m110) cc_final: 0.8001 (m-40) REVERT: N 295 ASN cc_start: 0.8360 (t0) cc_final: 0.7881 (m110) REVERT: N 305 GLU cc_start: 0.7059 (tt0) cc_final: 0.6634 (mt-10) REVERT: N 342 ASN cc_start: 0.7490 (m-40) cc_final: 0.6719 (t0) REVERT: N 352 GLN cc_start: 0.8474 (mm110) cc_final: 0.8138 (tt0) REVERT: N 375 GLU cc_start: 0.7830 (pt0) cc_final: 0.7343 (pm20) REVERT: N 393 GLN cc_start: 0.7281 (mt0) cc_final: 0.6579 (mp10) REVERT: N 402 ASN cc_start: 0.8355 (m-40) cc_final: 0.8065 (m-40) REVERT: N 413 LYS cc_start: 0.8304 (mtmt) cc_final: 0.8090 (mtpp) REVERT: N 512 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8491 (mm) REVERT: N 515 GLN cc_start: 0.7668 (mt0) cc_final: 0.7084 (mm-40) REVERT: O 286 LYS cc_start: 0.7722 (mttt) cc_final: 0.7374 (mtmt) REVERT: P 554 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7102 (tttm) outliers start: 79 outliers final: 55 residues processed: 540 average time/residue: 0.4526 time to fit residues: 370.9389 Evaluate side-chains 533 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 469 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 667 THR Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1189 SER Chi-restraints excluded: chain K residue 1191 LEU Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1294 MET Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain M residue 260 LYS Chi-restraints excluded: chain M residue 267 GLN Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 323 ILE Chi-restraints excluded: chain O residue 348 ASP Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 213 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 256 optimal weight: 0.0670 chunk 72 optimal weight: 0.1980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 27 GLN E 39 HIS E 68 GLN E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN K1137 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30094 Z= 0.151 Angle : 0.497 7.899 42067 Z= 0.284 Chirality : 0.035 0.163 4653 Planarity : 0.004 0.054 4165 Dihedral : 25.821 178.439 6658 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.58 % Allowed : 20.37 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.90 (0.17), residues: 2640 helix: 1.51 (0.14), residues: 1444 sheet: -0.74 (0.45), residues: 118 loop : -0.44 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 31 HIS 0.004 0.001 HIS E 39 PHE 0.022 0.001 PHE P 351 TYR 0.020 0.001 TYR F 88 ARG 0.007 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 489 time to evaluate : 2.962 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 90 MET cc_start: 0.7330 (tpp) cc_final: 0.6772 (tpp) REVERT: A 94 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 129 ARG cc_start: 0.7349 (tpt-90) cc_final: 0.7113 (tpt90) REVERT: B 31 LYS cc_start: 0.7229 (tttt) cc_final: 0.6920 (tttm) REVERT: B 92 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7579 (ttp80) REVERT: C 36 LYS cc_start: 0.8429 (mtmm) cc_final: 0.8131 (mtpt) REVERT: C 41 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7584 (mp0) REVERT: C 64 GLU cc_start: 0.7578 (tt0) cc_final: 0.6962 (tp30) REVERT: C 73 ASN cc_start: 0.8371 (t0) cc_final: 0.7935 (t0) REVERT: C 91 GLU cc_start: 0.7985 (tt0) cc_final: 0.7613 (tm-30) REVERT: C 116 LEU cc_start: 0.7384 (mm) cc_final: 0.6945 (mm) REVERT: D 39 TYR cc_start: 0.7639 (t80) cc_final: 0.7145 (t80) REVERT: D 46 HIS cc_start: 0.7105 (m-70) cc_final: 0.6499 (m-70) REVERT: D 65 ASP cc_start: 0.8623 (t0) cc_final: 0.8224 (t0) REVERT: D 68 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: D 81 ASN cc_start: 0.9052 (m110) cc_final: 0.8754 (m110) REVERT: D 82 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8821 (mmmt) REVERT: F 77 LYS cc_start: 0.8298 (mttt) cc_final: 0.7898 (mmtp) REVERT: F 79 LYS cc_start: 0.7886 (mttp) cc_final: 0.7457 (mmtm) REVERT: G 38 ASN cc_start: 0.7900 (m-40) cc_final: 0.7361 (m-40) REVERT: G 84 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7846 (tp-100) REVERT: G 104 GLN cc_start: 0.7401 (mp10) cc_final: 0.7187 (mp10) REVERT: H 39 TYR cc_start: 0.6369 (t80) cc_final: 0.6032 (t80) REVERT: H 52 SER cc_start: 0.8386 (t) cc_final: 0.8082 (p) REVERT: H 60 ASN cc_start: 0.6894 (t0) cc_final: 0.6613 (t0) REVERT: H 61 SER cc_start: 0.7766 (t) cc_final: 0.7207 (m) REVERT: H 64 ASN cc_start: 0.6815 (m110) cc_final: 0.6479 (m110) REVERT: H 82 LYS cc_start: 0.8562 (mmtp) cc_final: 0.8014 (mmmt) REVERT: K 670 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: K 764 PHE cc_start: 0.7326 (m-10) cc_final: 0.7020 (m-10) REVERT: K 816 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: K 860 MET cc_start: 0.7265 (mmm) cc_final: 0.6661 (mmt) REVERT: K 896 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7019 (ttpp) REVERT: K 982 LYS cc_start: 0.7910 (mttt) cc_final: 0.7328 (mtpt) REVERT: K 986 TYR cc_start: 0.7719 (m-10) cc_final: 0.7323 (m-10) REVERT: K 996 ILE cc_start: 0.7822 (mm) cc_final: 0.7559 (mt) REVERT: K 1008 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6725 (mt-10) REVERT: K 1015 LYS cc_start: 0.7269 (mttt) cc_final: 0.6782 (mptp) REVERT: K 1166 GLU cc_start: 0.7722 (pp20) cc_final: 0.7285 (pm20) REVERT: K 1182 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7294 (tppt) REVERT: K 1194 MET cc_start: 0.8188 (mtp) cc_final: 0.7839 (mtt) REVERT: K 1205 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7425 (mttm) REVERT: K 1210 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7785 (mt) REVERT: K 1244 LYS cc_start: 0.7456 (mmtt) cc_final: 0.7244 (mmtm) REVERT: K 1266 MET cc_start: 0.7951 (mmm) cc_final: 0.7558 (mmp) REVERT: K 1271 LYS cc_start: 0.7931 (mttt) cc_final: 0.7456 (ttmm) REVERT: K 1272 ASP cc_start: 0.7789 (t0) cc_final: 0.7511 (t70) REVERT: K 1285 ILE cc_start: 0.8740 (tp) cc_final: 0.8436 (tp) REVERT: K 1287 ARG cc_start: 0.7194 (ttm-80) cc_final: 0.6939 (ttp80) REVERT: L 53 MET cc_start: 0.9055 (mmp) cc_final: 0.8794 (mmp) REVERT: L 60 LYS cc_start: 0.8012 (mttm) cc_final: 0.7133 (mttp) REVERT: L 61 MET cc_start: 0.8841 (ptp) cc_final: 0.8519 (ptp) REVERT: L 96 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7201 (mtp) REVERT: L 98 LYS cc_start: 0.7551 (ptmt) cc_final: 0.7169 (tppt) REVERT: L 230 LYS cc_start: 0.8569 (tttm) cc_final: 0.8308 (tttp) REVERT: L 289 GLU cc_start: 0.8119 (mp0) cc_final: 0.7831 (mp0) REVERT: L 335 ASP cc_start: 0.7542 (p0) cc_final: 0.6727 (t70) REVERT: L 350 ASP cc_start: 0.8341 (p0) cc_final: 0.8107 (p0) REVERT: L 363 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8104 (m) REVERT: M 110 ARG cc_start: 0.9343 (tmm-80) cc_final: 0.9041 (tmm-80) REVERT: M 111 LEU cc_start: 0.8780 (mt) cc_final: 0.8214 (mt) REVERT: M 260 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7169 (ttpp) REVERT: M 308 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7189 (mm-30) REVERT: M 353 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6698 (mt0) REVERT: M 357 LYS cc_start: 0.7364 (tmtt) cc_final: 0.6950 (ttpt) REVERT: M 392 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8435 (p) REVERT: N 121 GLU cc_start: 0.7079 (mp0) cc_final: 0.6622 (mt-10) REVERT: N 175 MET cc_start: 0.6948 (mtt) cc_final: 0.6661 (ptp) REVERT: N 267 ASN cc_start: 0.8272 (m110) cc_final: 0.7985 (m-40) REVERT: N 295 ASN cc_start: 0.8338 (t0) cc_final: 0.7802 (m110) REVERT: N 305 GLU cc_start: 0.7060 (tt0) cc_final: 0.6628 (mt-10) REVERT: N 342 ASN cc_start: 0.7469 (m-40) cc_final: 0.6893 (t0) REVERT: N 352 GLN cc_start: 0.8425 (mm110) cc_final: 0.8197 (tt0) REVERT: N 375 GLU cc_start: 0.7814 (pt0) cc_final: 0.7338 (pm20) REVERT: N 393 GLN cc_start: 0.7284 (mt0) cc_final: 0.6698 (mp10) REVERT: N 402 ASN cc_start: 0.8346 (m-40) cc_final: 0.8064 (m-40) REVERT: N 413 LYS cc_start: 0.8303 (mtmt) cc_final: 0.8097 (mtpp) REVERT: N 512 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8410 (mm) REVERT: O 256 MET cc_start: 0.6197 (mmm) cc_final: 0.5924 (mmm) REVERT: O 311 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8106 (tptt) REVERT: P 554 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7050 (tttm) outliers start: 86 outliers final: 52 residues processed: 540 average time/residue: 0.4573 time to fit residues: 375.9320 Evaluate side-chains 536 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 472 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain M residue 94 TYR Chi-restraints excluded: chain M residue 260 LYS Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 392 SER Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 323 ILE Chi-restraints excluded: chain O residue 348 ASP Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 64 ASN F 75 HIS ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30094 Z= 0.360 Angle : 0.583 9.731 42067 Z= 0.326 Chirality : 0.040 0.234 4653 Planarity : 0.005 0.061 4165 Dihedral : 26.149 178.606 6658 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.83 % Allowed : 20.78 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2640 helix: 1.16 (0.14), residues: 1472 sheet: -0.64 (0.46), residues: 116 loop : -0.52 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K1151 HIS 0.006 0.001 HIS L 49 PHE 0.020 0.002 PHE M 17 TYR 0.020 0.002 TYR L 313 ARG 0.006 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 510 time to evaluate : 2.946 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 94 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: A 129 ARG cc_start: 0.7530 (tpt-90) cc_final: 0.7249 (tpt90) REVERT: B 31 LYS cc_start: 0.7241 (tttt) cc_final: 0.6935 (tttm) REVERT: C 36 LYS cc_start: 0.8403 (mtmm) cc_final: 0.8104 (mtpt) REVERT: C 64 GLU cc_start: 0.7595 (tt0) cc_final: 0.7173 (tp30) REVERT: C 73 ASN cc_start: 0.8344 (t0) cc_final: 0.7924 (t0) REVERT: C 91 GLU cc_start: 0.8048 (tt0) cc_final: 0.7677 (tm-30) REVERT: C 116 LEU cc_start: 0.7458 (mm) cc_final: 0.7006 (mm) REVERT: D 39 TYR cc_start: 0.7352 (t80) cc_final: 0.6953 (t80) REVERT: D 65 ASP cc_start: 0.8693 (t0) cc_final: 0.8306 (t0) REVERT: D 68 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: D 81 ASN cc_start: 0.8971 (m110) cc_final: 0.8663 (m110) REVERT: D 82 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8859 (mmmt) REVERT: F 44 LYS cc_start: 0.8369 (tttp) cc_final: 0.8150 (tptt) REVERT: F 77 LYS cc_start: 0.8369 (mttt) cc_final: 0.8017 (mmtp) REVERT: F 79 LYS cc_start: 0.7651 (mttp) cc_final: 0.7324 (mmtm) REVERT: F 88 TYR cc_start: 0.7015 (m-80) cc_final: 0.6742 (m-80) REVERT: G 84 GLN cc_start: 0.8134 (tp-100) cc_final: 0.7797 (tp-100) REVERT: H 39 TYR cc_start: 0.6669 (t80) cc_final: 0.6326 (t80) REVERT: H 52 SER cc_start: 0.8433 (t) cc_final: 0.8116 (p) REVERT: H 61 SER cc_start: 0.7784 (t) cc_final: 0.7249 (m) REVERT: H 82 LYS cc_start: 0.8591 (mmtp) cc_final: 0.8020 (mmmt) REVERT: H 90 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: K 670 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: K 707 ASP cc_start: 0.8052 (t0) cc_final: 0.7536 (t0) REVERT: K 721 LYS cc_start: 0.7645 (mttt) cc_final: 0.7367 (mtpp) REVERT: K 764 PHE cc_start: 0.7336 (m-10) cc_final: 0.7056 (m-10) REVERT: K 816 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: K 860 MET cc_start: 0.7414 (mmm) cc_final: 0.6646 (mmt) REVERT: K 896 LYS cc_start: 0.7669 (ttmt) cc_final: 0.7399 (ttpt) REVERT: K 903 GLU cc_start: 0.7556 (pp20) cc_final: 0.7299 (pp20) REVERT: K 982 LYS cc_start: 0.7876 (mttt) cc_final: 0.7353 (mtpt) REVERT: K 986 TYR cc_start: 0.7917 (m-80) cc_final: 0.7541 (m-80) REVERT: K 1015 LYS cc_start: 0.7364 (mttt) cc_final: 0.6926 (mttp) REVERT: K 1166 GLU cc_start: 0.7683 (pp20) cc_final: 0.7223 (pm20) REVERT: K 1182 LYS cc_start: 0.7547 (mmtt) cc_final: 0.7321 (tppt) REVERT: K 1194 MET cc_start: 0.8164 (mtp) cc_final: 0.7902 (mtt) REVERT: K 1205 LYS cc_start: 0.7805 (mmtt) cc_final: 0.7524 (mttm) REVERT: K 1244 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7264 (mmtm) REVERT: K 1256 LEU cc_start: 0.8322 (tt) cc_final: 0.7994 (tp) REVERT: K 1259 ASP cc_start: 0.6964 (t70) cc_final: 0.6609 (t70) REVERT: K 1271 LYS cc_start: 0.8046 (mttt) cc_final: 0.7486 (ttpp) REVERT: K 1272 ASP cc_start: 0.7919 (t0) cc_final: 0.7593 (t70) REVERT: K 1285 ILE cc_start: 0.8740 (tp) cc_final: 0.8430 (tp) REVERT: K 1287 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.7212 (ttp80) REVERT: L 60 LYS cc_start: 0.8092 (mttm) cc_final: 0.7316 (mttp) REVERT: L 61 MET cc_start: 0.9137 (ptp) cc_final: 0.8807 (ptp) REVERT: L 96 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7087 (mtp) REVERT: L 98 LYS cc_start: 0.7665 (ptmt) cc_final: 0.7191 (tppt) REVERT: L 230 LYS cc_start: 0.8535 (tttm) cc_final: 0.8266 (tttp) REVERT: L 335 ASP cc_start: 0.7516 (p0) cc_final: 0.6881 (t70) REVERT: L 336 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7122 (mttm) REVERT: L 363 VAL cc_start: 0.8692 (p) cc_final: 0.8390 (m) REVERT: M 111 LEU cc_start: 0.8787 (mt) cc_final: 0.8457 (mt) REVERT: M 238 TYR cc_start: 0.8443 (m-10) cc_final: 0.7233 (m-10) REVERT: M 277 GLN cc_start: 0.6606 (mm110) cc_final: 0.6320 (mt0) REVERT: M 308 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6942 (mm-30) REVERT: M 353 GLN cc_start: 0.7296 (mm-40) cc_final: 0.6787 (mt0) REVERT: M 354 LEU cc_start: 0.8145 (pp) cc_final: 0.7933 (tp) REVERT: M 357 LYS cc_start: 0.7492 (tmtt) cc_final: 0.7141 (tttp) REVERT: M 373 TYR cc_start: 0.8930 (m-80) cc_final: 0.8636 (m-80) REVERT: N 121 GLU cc_start: 0.7018 (mp0) cc_final: 0.6635 (mt-10) REVERT: N 267 ASN cc_start: 0.8304 (m110) cc_final: 0.8095 (m-40) REVERT: N 295 ASN cc_start: 0.8376 (t0) cc_final: 0.7949 (m110) REVERT: N 305 GLU cc_start: 0.7092 (tt0) cc_final: 0.6729 (mt-10) REVERT: N 342 ASN cc_start: 0.7784 (m-40) cc_final: 0.7029 (t0) REVERT: N 393 GLN cc_start: 0.7289 (mt0) cc_final: 0.6659 (mp10) REVERT: N 402 ASN cc_start: 0.8399 (m-40) cc_final: 0.7976 (m110) REVERT: N 413 LYS cc_start: 0.8280 (mtmt) cc_final: 0.8050 (mtpp) REVERT: N 436 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8980 (mt) REVERT: N 512 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8721 (mt) REVERT: N 515 GLN cc_start: 0.7937 (mt0) cc_final: 0.7209 (mm-40) REVERT: O 244 LYS cc_start: 0.4224 (tptp) cc_final: 0.3939 (tptp) REVERT: O 256 MET cc_start: 0.6346 (mmm) cc_final: 0.5986 (mmm) REVERT: O 260 LYS cc_start: 0.7687 (ptmt) cc_final: 0.7165 (ptmt) REVERT: O 292 CYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7748 (t) REVERT: O 308 GLU cc_start: 0.7963 (tp30) cc_final: 0.7667 (tp30) REVERT: O 310 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8621 (mp) REVERT: O 311 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8166 (tptt) REVERT: O 372 GLU cc_start: 0.8344 (tp30) cc_final: 0.7801 (tp30) REVERT: P 320 LYS cc_start: 0.8533 (mttt) cc_final: 0.7999 (mtmt) REVERT: P 557 LYS cc_start: 0.7292 (mmtm) cc_final: 0.6688 (mmtm) outliers start: 92 outliers final: 70 residues processed: 572 average time/residue: 0.4818 time to fit residues: 426.8835 Evaluate side-chains 583 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 502 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 667 THR Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 718 THR Chi-restraints excluded: chain K residue 779 ASN Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 844 ASN Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 94 TYR Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain N residue 360 THR Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 436 LEU Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain N residue 499 ASN Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 323 ILE Chi-restraints excluded: chain O residue 348 ASP Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Chi-restraints excluded: chain P residue 555 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 241 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 38 ASN M 18 HIS ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30094 Z= 0.289 Angle : 0.554 8.215 42067 Z= 0.311 Chirality : 0.038 0.168 4653 Planarity : 0.004 0.044 4165 Dihedral : 26.032 179.623 6658 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.75 % Allowed : 21.53 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2640 helix: 1.24 (0.14), residues: 1469 sheet: -0.64 (0.46), residues: 116 loop : -0.48 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K1151 HIS 0.005 0.001 HIS L 49 PHE 0.022 0.002 PHE M 17 TYR 0.029 0.002 TYR F 88 ARG 0.007 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 506 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8716 (tt) cc_final: 0.8442 (tp) REVERT: A 85 GLN cc_start: 0.8080 (mt0) cc_final: 0.7419 (mt0) REVERT: A 94 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: A 129 ARG cc_start: 0.7414 (tpt-90) cc_final: 0.7139 (tpt90) REVERT: B 31 LYS cc_start: 0.7199 (tttt) cc_final: 0.6911 (tttm) REVERT: C 36 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8102 (mtpt) REVERT: C 56 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6765 (tm-30) REVERT: C 64 GLU cc_start: 0.7601 (tt0) cc_final: 0.7154 (tp30) REVERT: C 73 ASN cc_start: 0.8359 (t0) cc_final: 0.7899 (t0) REVERT: C 92 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7286 (mm-30) REVERT: C 116 LEU cc_start: 0.7446 (mm) cc_final: 0.6976 (mm) REVERT: D 39 TYR cc_start: 0.7460 (t80) cc_final: 0.6988 (t80) REVERT: D 65 ASP cc_start: 0.8678 (t0) cc_final: 0.8290 (t0) REVERT: D 68 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: D 81 ASN cc_start: 0.8984 (m110) cc_final: 0.8658 (m110) REVERT: D 82 LYS cc_start: 0.9063 (mmtt) cc_final: 0.8853 (mmmt) REVERT: F 44 LYS cc_start: 0.8447 (tttp) cc_final: 0.8240 (tttp) REVERT: F 77 LYS cc_start: 0.8308 (mttt) cc_final: 0.7949 (mmtp) REVERT: F 79 LYS cc_start: 0.7663 (mttp) cc_final: 0.7346 (mmtm) REVERT: F 88 TYR cc_start: 0.7163 (m-80) cc_final: 0.6557 (m-80) REVERT: G 84 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7844 (tp-100) REVERT: H 39 TYR cc_start: 0.6622 (t80) cc_final: 0.6261 (t80) REVERT: H 44 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7500 (tm-30) REVERT: H 52 SER cc_start: 0.8396 (t) cc_final: 0.8096 (p) REVERT: H 60 ASN cc_start: 0.7060 (t0) cc_final: 0.6836 (t0) REVERT: H 61 SER cc_start: 0.7760 (t) cc_final: 0.7230 (m) REVERT: H 64 ASN cc_start: 0.6664 (m110) cc_final: 0.6311 (m110) REVERT: H 82 LYS cc_start: 0.8577 (mmtp) cc_final: 0.8023 (mmmt) REVERT: H 90 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: K 670 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7275 (pm20) REVERT: K 721 LYS cc_start: 0.7670 (mttt) cc_final: 0.7341 (mtpp) REVERT: K 764 PHE cc_start: 0.7363 (m-10) cc_final: 0.7085 (m-10) REVERT: K 816 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: K 860 MET cc_start: 0.7339 (mmm) cc_final: 0.6700 (mmt) REVERT: K 896 LYS cc_start: 0.7623 (ttmt) cc_final: 0.7349 (ttpt) REVERT: K 903 GLU cc_start: 0.7537 (pp20) cc_final: 0.7280 (pp20) REVERT: K 982 LYS cc_start: 0.7849 (mttt) cc_final: 0.7276 (mtpt) REVERT: K 986 TYR cc_start: 0.7901 (m-80) cc_final: 0.7530 (m-80) REVERT: K 1015 LYS cc_start: 0.7398 (mttt) cc_final: 0.6921 (mttp) REVERT: K 1166 GLU cc_start: 0.7713 (pp20) cc_final: 0.7267 (pm20) REVERT: K 1167 ARG cc_start: 0.7298 (ttp80) cc_final: 0.6948 (ttp80) REVERT: K 1182 LYS cc_start: 0.7539 (mmtt) cc_final: 0.7318 (tppt) REVERT: K 1194 MET cc_start: 0.8198 (mtp) cc_final: 0.7756 (mtt) REVERT: K 1205 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7510 (mttm) REVERT: K 1244 LYS cc_start: 0.7500 (mmtt) cc_final: 0.7192 (mmtm) REVERT: K 1256 LEU cc_start: 0.8365 (tt) cc_final: 0.8076 (tp) REVERT: K 1259 ASP cc_start: 0.6902 (t70) cc_final: 0.6618 (t70) REVERT: K 1271 LYS cc_start: 0.7955 (mttt) cc_final: 0.7456 (mttm) REVERT: K 1272 ASP cc_start: 0.7918 (t0) cc_final: 0.7573 (t70) REVERT: K 1285 ILE cc_start: 0.8735 (tp) cc_final: 0.8408 (tp) REVERT: K 1287 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7189 (ttp80) REVERT: L 60 LYS cc_start: 0.8069 (mttm) cc_final: 0.7332 (mttp) REVERT: L 61 MET cc_start: 0.9068 (ptp) cc_final: 0.8724 (ptp) REVERT: L 96 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7163 (mtp) REVERT: L 98 LYS cc_start: 0.7637 (ptmt) cc_final: 0.7149 (tppt) REVERT: L 114 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6637 (p0) REVERT: L 230 LYS cc_start: 0.8561 (tttm) cc_final: 0.8289 (tttp) REVERT: L 335 ASP cc_start: 0.7555 (p0) cc_final: 0.6882 (t70) REVERT: L 363 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8385 (m) REVERT: M 111 LEU cc_start: 0.8774 (mt) cc_final: 0.8357 (mt) REVERT: M 238 TYR cc_start: 0.8418 (m-10) cc_final: 0.7113 (m-80) REVERT: M 277 GLN cc_start: 0.6661 (mm110) cc_final: 0.6337 (mt0) REVERT: M 296 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7121 (ppp) REVERT: M 308 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7068 (mm-30) REVERT: M 353 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6775 (mt0) REVERT: M 357 LYS cc_start: 0.7428 (tmtt) cc_final: 0.7077 (tttp) REVERT: M 373 TYR cc_start: 0.8841 (m-80) cc_final: 0.8498 (m-80) REVERT: N 107 LYS cc_start: 0.7433 (mmtp) cc_final: 0.7013 (mmtp) REVERT: N 121 GLU cc_start: 0.7043 (mp0) cc_final: 0.6656 (mt-10) REVERT: N 267 ASN cc_start: 0.8287 (m110) cc_final: 0.8046 (m-40) REVERT: N 295 ASN cc_start: 0.8394 (t0) cc_final: 0.8003 (m110) REVERT: N 305 GLU cc_start: 0.7105 (tt0) cc_final: 0.6724 (mt-10) REVERT: N 342 ASN cc_start: 0.7779 (m-40) cc_final: 0.7035 (t0) REVERT: N 393 GLN cc_start: 0.7306 (mt0) cc_final: 0.6673 (mp10) REVERT: N 402 ASN cc_start: 0.8365 (m-40) cc_final: 0.7913 (m-40) REVERT: N 413 LYS cc_start: 0.8299 (mtmt) cc_final: 0.8064 (mtpp) REVERT: N 512 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8707 (mt) REVERT: N 515 GLN cc_start: 0.7891 (mt0) cc_final: 0.7174 (mm-40) REVERT: O 244 LYS cc_start: 0.4245 (tptp) cc_final: 0.3821 (tptp) REVERT: O 255 GLU cc_start: 0.6753 (tt0) cc_final: 0.6534 (tt0) REVERT: O 256 MET cc_start: 0.6272 (mmm) cc_final: 0.5876 (mmm) REVERT: O 292 CYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7789 (t) REVERT: O 308 GLU cc_start: 0.7962 (tp30) cc_final: 0.7643 (tp30) REVERT: O 309 LEU cc_start: 0.8673 (mm) cc_final: 0.8338 (mp) REVERT: O 311 LYS cc_start: 0.8287 (mtmm) cc_final: 0.8033 (tptt) REVERT: O 372 GLU cc_start: 0.8376 (tp30) cc_final: 0.7830 (tp30) REVERT: P 320 LYS cc_start: 0.8565 (mttt) cc_final: 0.8010 (mtmt) REVERT: P 557 LYS cc_start: 0.7306 (mmtm) cc_final: 0.6766 (mmtm) outliers start: 90 outliers final: 64 residues processed: 569 average time/residue: 0.4432 time to fit residues: 385.0004 Evaluate side-chains 574 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 499 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 844 ASN Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1294 MET Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain M residue 94 TYR Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 499 ASN Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 323 ILE Chi-restraints excluded: chain O residue 348 ASP Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 chunk 85 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 194 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 224 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 38 ASN G 68 ASN ** K 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 HIS ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30094 Z= 0.194 Angle : 0.530 9.622 42067 Z= 0.298 Chirality : 0.037 0.187 4653 Planarity : 0.004 0.044 4165 Dihedral : 25.865 179.806 6658 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.12 % Allowed : 22.45 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.85 (0.17), residues: 2640 helix: 1.44 (0.14), residues: 1459 sheet: -0.68 (0.44), residues: 128 loop : -0.45 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 464 HIS 0.003 0.001 HIS M 18 PHE 0.025 0.001 PHE M 17 TYR 0.022 0.001 TYR F 88 ARG 0.007 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 496 time to evaluate : 2.591 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 74 ILE cc_start: 0.8720 (tt) cc_final: 0.8432 (tp) REVERT: A 85 GLN cc_start: 0.8116 (mt0) cc_final: 0.7371 (mt0) REVERT: A 90 MET cc_start: 0.7383 (tpp) cc_final: 0.6857 (tpp) REVERT: A 94 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: A 129 ARG cc_start: 0.7221 (tpt-90) cc_final: 0.6955 (tpt90) REVERT: B 31 LYS cc_start: 0.7233 (tttt) cc_final: 0.6940 (tttm) REVERT: C 36 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8130 (mtpt) REVERT: C 56 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6732 (tm-30) REVERT: C 64 GLU cc_start: 0.7563 (tt0) cc_final: 0.7093 (tp30) REVERT: C 73 ASN cc_start: 0.8360 (t0) cc_final: 0.7920 (t0) REVERT: C 116 LEU cc_start: 0.7291 (mm) cc_final: 0.6799 (mm) REVERT: D 39 TYR cc_start: 0.7472 (t80) cc_final: 0.6937 (t80) REVERT: D 65 ASP cc_start: 0.8645 (t0) cc_final: 0.8227 (t0) REVERT: D 81 ASN cc_start: 0.8982 (m110) cc_final: 0.8691 (m110) REVERT: F 44 LYS cc_start: 0.8435 (tttp) cc_final: 0.8194 (tttp) REVERT: F 77 LYS cc_start: 0.8294 (mttt) cc_final: 0.7943 (mmtp) REVERT: F 79 LYS cc_start: 0.7855 (mttp) cc_final: 0.7438 (mmtm) REVERT: F 88 TYR cc_start: 0.7167 (m-80) cc_final: 0.6587 (m-80) REVERT: G 84 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7833 (tp-100) REVERT: H 39 TYR cc_start: 0.6455 (t80) cc_final: 0.6079 (t80) REVERT: H 52 SER cc_start: 0.8376 (t) cc_final: 0.8078 (p) REVERT: H 60 ASN cc_start: 0.7044 (t0) cc_final: 0.6815 (t0) REVERT: H 61 SER cc_start: 0.7740 (t) cc_final: 0.7236 (m) REVERT: H 64 ASN cc_start: 0.6664 (m110) cc_final: 0.6304 (m110) REVERT: H 82 LYS cc_start: 0.8579 (mmtp) cc_final: 0.7999 (mmmt) REVERT: H 90 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: K 670 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7275 (pm20) REVERT: K 721 LYS cc_start: 0.7713 (mttt) cc_final: 0.7429 (mtpp) REVERT: K 764 PHE cc_start: 0.7338 (m-10) cc_final: 0.7078 (m-10) REVERT: K 816 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: K 860 MET cc_start: 0.7302 (mmm) cc_final: 0.6660 (mmt) REVERT: K 896 LYS cc_start: 0.7557 (ttmt) cc_final: 0.7288 (ttpt) REVERT: K 903 GLU cc_start: 0.7516 (pp20) cc_final: 0.7293 (pp20) REVERT: K 982 LYS cc_start: 0.7766 (mttt) cc_final: 0.7246 (mmtp) REVERT: K 986 TYR cc_start: 0.7871 (m-80) cc_final: 0.7464 (m-80) REVERT: K 996 ILE cc_start: 0.7724 (mm) cc_final: 0.7518 (mt) REVERT: K 1015 LYS cc_start: 0.7341 (mttt) cc_final: 0.6832 (mptp) REVERT: K 1166 GLU cc_start: 0.7770 (pp20) cc_final: 0.7288 (pm20) REVERT: K 1182 LYS cc_start: 0.7558 (mmtt) cc_final: 0.7333 (tppt) REVERT: K 1194 MET cc_start: 0.8236 (mtp) cc_final: 0.7815 (mtt) REVERT: K 1205 LYS cc_start: 0.7769 (mmtt) cc_final: 0.7477 (mttm) REVERT: K 1210 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7729 (mt) REVERT: K 1244 LYS cc_start: 0.7470 (mmtt) cc_final: 0.7241 (mmtm) REVERT: K 1256 LEU cc_start: 0.8355 (tt) cc_final: 0.8075 (tp) REVERT: K 1259 ASP cc_start: 0.6934 (t70) cc_final: 0.6638 (t70) REVERT: K 1271 LYS cc_start: 0.7950 (mttt) cc_final: 0.7500 (mttm) REVERT: K 1272 ASP cc_start: 0.7894 (t0) cc_final: 0.7567 (t70) REVERT: K 1285 ILE cc_start: 0.8733 (tp) cc_final: 0.8414 (tp) REVERT: K 1287 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7159 (ttp80) REVERT: L 60 LYS cc_start: 0.8069 (mttm) cc_final: 0.7338 (mttt) REVERT: L 61 MET cc_start: 0.8943 (ptp) cc_final: 0.8621 (ptp) REVERT: L 96 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7172 (mtp) REVERT: L 98 LYS cc_start: 0.7608 (ptmt) cc_final: 0.7134 (tppt) REVERT: L 114 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6567 (p0) REVERT: L 230 LYS cc_start: 0.8552 (tttm) cc_final: 0.8290 (tttp) REVERT: L 335 ASP cc_start: 0.7524 (p0) cc_final: 0.6769 (t70) REVERT: M 238 TYR cc_start: 0.8366 (m-10) cc_final: 0.7044 (m-80) REVERT: M 277 GLN cc_start: 0.6674 (mm110) cc_final: 0.6366 (mt0) REVERT: M 296 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.6835 (ppp) REVERT: M 308 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7187 (mm-30) REVERT: M 353 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6699 (mt0) REVERT: M 357 LYS cc_start: 0.7328 (tmtt) cc_final: 0.7009 (tttp) REVERT: N 107 LYS cc_start: 0.7285 (mmtp) cc_final: 0.7083 (mttp) REVERT: N 121 GLU cc_start: 0.7035 (mp0) cc_final: 0.6641 (mt-10) REVERT: N 175 MET cc_start: 0.7025 (mtt) cc_final: 0.6674 (ptp) REVERT: N 267 ASN cc_start: 0.8257 (m110) cc_final: 0.8048 (m-40) REVERT: N 295 ASN cc_start: 0.8435 (t0) cc_final: 0.8103 (m110) REVERT: N 305 GLU cc_start: 0.7106 (tt0) cc_final: 0.6722 (mt-10) REVERT: N 342 ASN cc_start: 0.7744 (m-40) cc_final: 0.7257 (t0) REVERT: N 393 GLN cc_start: 0.7318 (mt0) cc_final: 0.6799 (mp10) REVERT: N 402 ASN cc_start: 0.8338 (m-40) cc_final: 0.7878 (m-40) REVERT: N 413 LYS cc_start: 0.8300 (mtmt) cc_final: 0.8072 (mtpp) REVERT: N 512 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8718 (mt) REVERT: N 515 GLN cc_start: 0.7845 (mt0) cc_final: 0.7134 (mm-40) REVERT: O 256 MET cc_start: 0.6249 (mmm) cc_final: 0.5978 (mmm) REVERT: O 291 LYS cc_start: 0.8154 (tmtt) cc_final: 0.7609 (tmtt) REVERT: O 292 CYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7756 (t) REVERT: O 309 LEU cc_start: 0.8656 (mm) cc_final: 0.8296 (mp) REVERT: P 557 LYS cc_start: 0.7289 (mmtm) cc_final: 0.6718 (mmtm) outliers start: 75 outliers final: 55 residues processed: 543 average time/residue: 0.4487 time to fit residues: 370.8727 Evaluate side-chains 552 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 487 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 844 ASN Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1160 GLU Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1294 MET Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 499 ASN Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 323 ILE Chi-restraints excluded: chain O residue 348 ASP Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 0.4980 chunk 273 optimal weight: 20.0000 chunk 249 optimal weight: 5.9990 chunk 265 optimal weight: 40.0000 chunk 160 optimal weight: 0.0980 chunk 115 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 240 optimal weight: 0.0060 chunk 251 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 38 ASN ** K 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 HIS ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30094 Z= 0.226 Angle : 0.546 8.292 42067 Z= 0.306 Chirality : 0.038 0.264 4653 Planarity : 0.004 0.043 4165 Dihedral : 25.887 179.781 6658 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.12 % Allowed : 22.20 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.85 (0.16), residues: 2640 helix: 1.43 (0.14), residues: 1467 sheet: -0.73 (0.45), residues: 118 loop : -0.45 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 261 HIS 0.007 0.001 HIS E 39 PHE 0.028 0.001 PHE M 17 TYR 0.022 0.002 TYR F 88 ARG 0.007 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 488 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.8492 (m) cc_final: 0.8120 (t) REVERT: A 74 ILE cc_start: 0.8717 (tt) cc_final: 0.8412 (tp) REVERT: A 90 MET cc_start: 0.7385 (tpp) cc_final: 0.6836 (tpp) REVERT: A 94 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: A 129 ARG cc_start: 0.7240 (tpt-90) cc_final: 0.6959 (tpt90) REVERT: B 31 LYS cc_start: 0.7301 (tttt) cc_final: 0.7008 (tttm) REVERT: C 36 LYS cc_start: 0.8494 (mtmm) cc_final: 0.8195 (mtpt) REVERT: C 56 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6752 (tm-30) REVERT: C 64 GLU cc_start: 0.7571 (tt0) cc_final: 0.7108 (tp30) REVERT: C 73 ASN cc_start: 0.8365 (t0) cc_final: 0.7884 (t0) REVERT: C 92 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7251 (mm-30) REVERT: C 116 LEU cc_start: 0.7292 (mm) cc_final: 0.6798 (mm) REVERT: D 39 TYR cc_start: 0.7452 (t80) cc_final: 0.6953 (t80) REVERT: D 65 ASP cc_start: 0.8651 (t0) cc_final: 0.8220 (t0) REVERT: D 81 ASN cc_start: 0.8970 (m110) cc_final: 0.8684 (m110) REVERT: F 77 LYS cc_start: 0.8303 (mttt) cc_final: 0.7958 (mmtp) REVERT: F 79 LYS cc_start: 0.7855 (mttp) cc_final: 0.7436 (mmtm) REVERT: G 84 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7821 (tp-100) REVERT: H 39 TYR cc_start: 0.6461 (t80) cc_final: 0.6073 (t80) REVERT: H 52 SER cc_start: 0.8395 (t) cc_final: 0.8103 (p) REVERT: H 60 ASN cc_start: 0.7038 (t0) cc_final: 0.6804 (t0) REVERT: H 61 SER cc_start: 0.7744 (t) cc_final: 0.7237 (m) REVERT: H 64 ASN cc_start: 0.6689 (m110) cc_final: 0.6331 (m110) REVERT: H 82 LYS cc_start: 0.8573 (mmtp) cc_final: 0.7994 (mmmt) REVERT: H 90 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: K 670 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7267 (pm20) REVERT: K 721 LYS cc_start: 0.7699 (mttt) cc_final: 0.7410 (mtpp) REVERT: K 764 PHE cc_start: 0.7356 (m-10) cc_final: 0.7058 (m-10) REVERT: K 816 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: K 860 MET cc_start: 0.7326 (mmm) cc_final: 0.6687 (mmt) REVERT: K 896 LYS cc_start: 0.7570 (ttmt) cc_final: 0.7301 (ttpt) REVERT: K 903 GLU cc_start: 0.7509 (pp20) cc_final: 0.7301 (pp20) REVERT: K 982 LYS cc_start: 0.7790 (mttt) cc_final: 0.7274 (mmtp) REVERT: K 986 TYR cc_start: 0.7897 (m-80) cc_final: 0.7515 (m-80) REVERT: K 1015 LYS cc_start: 0.7348 (mttt) cc_final: 0.6841 (mptp) REVERT: K 1166 GLU cc_start: 0.7785 (pp20) cc_final: 0.7293 (pm20) REVERT: K 1167 ARG cc_start: 0.7310 (ttp80) cc_final: 0.6947 (ttp80) REVERT: K 1194 MET cc_start: 0.8234 (mtp) cc_final: 0.7801 (mtt) REVERT: K 1205 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7484 (mttm) REVERT: K 1210 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7656 (mt) REVERT: K 1244 LYS cc_start: 0.7474 (mmtt) cc_final: 0.7249 (mmtm) REVERT: K 1256 LEU cc_start: 0.8418 (tt) cc_final: 0.8124 (tp) REVERT: K 1259 ASP cc_start: 0.6951 (t70) cc_final: 0.6657 (t70) REVERT: K 1271 LYS cc_start: 0.7926 (mttt) cc_final: 0.7450 (mttm) REVERT: K 1272 ASP cc_start: 0.7876 (t0) cc_final: 0.7531 (t70) REVERT: K 1285 ILE cc_start: 0.8726 (tp) cc_final: 0.8406 (tp) REVERT: K 1287 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.7156 (ttp80) REVERT: L 60 LYS cc_start: 0.8067 (mttm) cc_final: 0.7338 (mttp) REVERT: L 61 MET cc_start: 0.9037 (ptp) cc_final: 0.8698 (ptp) REVERT: L 96 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7155 (mtp) REVERT: L 98 LYS cc_start: 0.7631 (ptmt) cc_final: 0.7147 (tppt) REVERT: L 230 LYS cc_start: 0.8560 (tttm) cc_final: 0.8287 (tttp) REVERT: L 335 ASP cc_start: 0.7542 (p0) cc_final: 0.6774 (t70) REVERT: M 238 TYR cc_start: 0.8382 (m-10) cc_final: 0.7064 (m-80) REVERT: M 277 GLN cc_start: 0.6678 (mm110) cc_final: 0.6369 (mt0) REVERT: M 296 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.6903 (ppp) REVERT: M 308 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7158 (mm-30) REVERT: M 353 GLN cc_start: 0.7253 (mm-40) cc_final: 0.6759 (mt0) REVERT: M 357 LYS cc_start: 0.7340 (tmtt) cc_final: 0.7024 (tttp) REVERT: N 121 GLU cc_start: 0.7044 (mp0) cc_final: 0.6657 (mt-10) REVERT: N 175 MET cc_start: 0.6999 (mtt) cc_final: 0.6677 (ptp) REVERT: N 267 ASN cc_start: 0.8261 (m110) cc_final: 0.8056 (m-40) REVERT: N 295 ASN cc_start: 0.8441 (t0) cc_final: 0.8120 (m110) REVERT: N 305 GLU cc_start: 0.7107 (tt0) cc_final: 0.6722 (mt-10) REVERT: N 342 ASN cc_start: 0.7743 (m-40) cc_final: 0.7067 (t0) REVERT: N 393 GLN cc_start: 0.7335 (mt0) cc_final: 0.6819 (mp10) REVERT: N 402 ASN cc_start: 0.8378 (m-40) cc_final: 0.7917 (m-40) REVERT: N 413 LYS cc_start: 0.8295 (mtmt) cc_final: 0.8066 (mtpp) REVERT: N 515 GLN cc_start: 0.7857 (mt0) cc_final: 0.7145 (mm-40) REVERT: O 256 MET cc_start: 0.6258 (mmm) cc_final: 0.6006 (mmm) REVERT: O 286 LYS cc_start: 0.7942 (mttt) cc_final: 0.7662 (mtmt) REVERT: O 291 LYS cc_start: 0.8300 (tmtt) cc_final: 0.7774 (tmtt) REVERT: O 292 CYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7766 (t) REVERT: P 557 LYS cc_start: 0.7290 (mmtm) cc_final: 0.6715 (mmtm) outliers start: 75 outliers final: 58 residues processed: 539 average time/residue: 0.4580 time to fit residues: 374.0001 Evaluate side-chains 553 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 487 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 844 ASN Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1294 MET Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 499 ASN Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 323 ILE Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.6980 chunk 281 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 195 optimal weight: 0.4980 chunk 294 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 234 optimal weight: 10.0000 chunk 24 optimal weight: 0.0010 chunk 181 optimal weight: 0.6980 chunk 143 optimal weight: 20.0000 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 38 ASN ** K 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 779 ASN M 18 HIS ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 422 GLN O 275 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30094 Z= 0.161 Angle : 0.523 8.773 42067 Z= 0.294 Chirality : 0.036 0.209 4653 Planarity : 0.004 0.044 4165 Dihedral : 25.729 179.997 6658 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.54 % Allowed : 22.95 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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 (0.17), residues: 2640 helix: 1.60 (0.14), residues: 1458 sheet: -0.59 (0.44), residues: 127 loop : -0.36 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 464 HIS 0.007 0.001 HIS E 39 PHE 0.024 0.001 PHE M 17 TYR 0.018 0.001 TYR F 88 ARG 0.007 0.000 ARG B 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 498 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.8535 (m) cc_final: 0.8156 (t) REVERT: A 74 ILE cc_start: 0.8726 (tt) cc_final: 0.8459 (tp) REVERT: A 85 GLN cc_start: 0.8001 (mt0) cc_final: 0.7253 (mt0) REVERT: A 94 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: A 129 ARG cc_start: 0.7131 (tpt-90) cc_final: 0.6826 (tpt90) REVERT: B 31 LYS cc_start: 0.7319 (tttt) cc_final: 0.7013 (tttm) REVERT: C 36 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8205 (mtpt) REVERT: C 56 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6746 (tm-30) REVERT: C 64 GLU cc_start: 0.7479 (tt0) cc_final: 0.6951 (tp30) REVERT: C 73 ASN cc_start: 0.8340 (t0) cc_final: 0.7875 (t0) REVERT: C 92 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7167 (mm-30) REVERT: D 39 TYR cc_start: 0.7538 (t80) cc_final: 0.6997 (t80) REVERT: D 40 LYS cc_start: 0.7468 (mtpp) cc_final: 0.7216 (mtpt) REVERT: D 65 ASP cc_start: 0.8636 (t0) cc_final: 0.8232 (t0) REVERT: E 39 HIS cc_start: 0.8469 (t70) cc_final: 0.8250 (t-90) REVERT: F 77 LYS cc_start: 0.8246 (mttt) cc_final: 0.7904 (mmtp) REVERT: F 79 LYS cc_start: 0.7881 (mttp) cc_final: 0.7433 (mmtm) REVERT: G 84 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7821 (tp-100) REVERT: H 39 TYR cc_start: 0.6295 (t80) cc_final: 0.5881 (t80) REVERT: H 52 SER cc_start: 0.8209 (t) cc_final: 0.7954 (p) REVERT: H 60 ASN cc_start: 0.6942 (t0) cc_final: 0.6679 (t0) REVERT: H 61 SER cc_start: 0.7685 (t) cc_final: 0.7206 (m) REVERT: H 64 ASN cc_start: 0.6661 (m110) cc_final: 0.6299 (m110) REVERT: H 82 LYS cc_start: 0.8551 (mmtp) cc_final: 0.8324 (mppt) REVERT: H 90 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: K 670 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: K 721 LYS cc_start: 0.7662 (mttt) cc_final: 0.7412 (mtpp) REVERT: K 764 PHE cc_start: 0.7317 (m-10) cc_final: 0.7008 (m-10) REVERT: K 816 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: K 860 MET cc_start: 0.7255 (mmm) cc_final: 0.6639 (mmt) REVERT: K 896 LYS cc_start: 0.7537 (ttmt) cc_final: 0.7008 (ttpp) REVERT: K 903 GLU cc_start: 0.7480 (pp20) cc_final: 0.7238 (pp20) REVERT: K 982 LYS cc_start: 0.7757 (mttt) cc_final: 0.7276 (mmtp) REVERT: K 986 TYR cc_start: 0.7814 (m-80) cc_final: 0.7388 (m-10) REVERT: K 996 ILE cc_start: 0.7710 (mm) cc_final: 0.7482 (mt) REVERT: K 1015 LYS cc_start: 0.7313 (mttt) cc_final: 0.6810 (mptp) REVERT: K 1167 ARG cc_start: 0.7245 (ttp80) cc_final: 0.6879 (ttp80) REVERT: K 1194 MET cc_start: 0.8171 (mtp) cc_final: 0.7784 (mtt) REVERT: K 1205 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7460 (mttm) REVERT: K 1210 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7726 (mt) REVERT: K 1244 LYS cc_start: 0.7441 (mmtt) cc_final: 0.7215 (mmtm) REVERT: K 1256 LEU cc_start: 0.8296 (tt) cc_final: 0.8015 (tp) REVERT: K 1259 ASP cc_start: 0.6687 (t70) cc_final: 0.6397 (t70) REVERT: K 1271 LYS cc_start: 0.7905 (mttt) cc_final: 0.7410 (ttmm) REVERT: K 1272 ASP cc_start: 0.7854 (t0) cc_final: 0.7558 (t70) REVERT: K 1285 ILE cc_start: 0.8801 (tp) cc_final: 0.8474 (tp) REVERT: K 1287 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.7126 (ttp80) REVERT: L 60 LYS cc_start: 0.8039 (mttm) cc_final: 0.7198 (mttp) REVERT: L 61 MET cc_start: 0.8879 (ptp) cc_final: 0.8537 (ptp) REVERT: L 96 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7185 (mtp) REVERT: L 98 LYS cc_start: 0.7578 (ptmt) cc_final: 0.7126 (tppt) REVERT: L 230 LYS cc_start: 0.8528 (tttm) cc_final: 0.8262 (tttp) REVERT: L 260 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6956 (mm-30) REVERT: L 289 GLU cc_start: 0.8047 (mp0) cc_final: 0.7837 (mp0) REVERT: L 335 ASP cc_start: 0.7596 (p0) cc_final: 0.6785 (t70) REVERT: M 13 ARG cc_start: 0.7840 (mtp85) cc_final: 0.6500 (ptp-170) REVERT: M 22 MET cc_start: 0.2720 (mmp) cc_final: 0.2491 (mmt) REVERT: M 111 LEU cc_start: 0.8523 (mt) cc_final: 0.8259 (mt) REVERT: M 277 GLN cc_start: 0.6716 (mm110) cc_final: 0.6463 (mt0) REVERT: M 296 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.6863 (ppp) REVERT: M 308 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7160 (mm-30) REVERT: M 353 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6674 (mt0) REVERT: M 357 LYS cc_start: 0.7294 (tmtt) cc_final: 0.6973 (tttp) REVERT: N 107 LYS cc_start: 0.7089 (mttp) cc_final: 0.6632 (mttp) REVERT: N 121 GLU cc_start: 0.7049 (mp0) cc_final: 0.6629 (mt-10) REVERT: N 175 MET cc_start: 0.6980 (mtt) cc_final: 0.6733 (ptp) REVERT: N 267 ASN cc_start: 0.8304 (m110) cc_final: 0.8033 (m-40) REVERT: N 295 ASN cc_start: 0.8429 (t0) cc_final: 0.8130 (m110) REVERT: N 305 GLU cc_start: 0.7108 (tt0) cc_final: 0.6717 (mt-10) REVERT: N 342 ASN cc_start: 0.7684 (m-40) cc_final: 0.7074 (t0) REVERT: N 352 GLN cc_start: 0.8442 (mm110) cc_final: 0.8205 (tt0) REVERT: N 402 ASN cc_start: 0.8333 (m-40) cc_final: 0.7872 (m-40) REVERT: N 413 LYS cc_start: 0.8302 (mtmt) cc_final: 0.8074 (mtpp) REVERT: N 515 GLN cc_start: 0.7762 (mt0) cc_final: 0.7531 (mm-40) REVERT: O 256 MET cc_start: 0.6192 (mmm) cc_final: 0.5972 (mmm) REVERT: O 286 LYS cc_start: 0.7924 (mttt) cc_final: 0.7632 (mtmt) REVERT: O 291 LYS cc_start: 0.8144 (tmtt) cc_final: 0.7665 (tmtt) REVERT: O 311 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8186 (tptt) REVERT: P 557 LYS cc_start: 0.7238 (mmtm) cc_final: 0.6680 (mmtm) outliers start: 61 outliers final: 45 residues processed: 537 average time/residue: 0.4572 time to fit residues: 374.8550 Evaluate side-chains 543 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 491 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 844 ASN Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 240 ASP Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 499 ASN Chi-restraints excluded: chain O residue 274 SER Chi-restraints excluded: chain O residue 323 ILE Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 235 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 241 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 43 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 38 ASN ** K 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.198593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.129093 restraints weight = 36921.848| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.10 r_work: 0.3125 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30094 Z= 0.256 Angle : 0.559 9.241 42067 Z= 0.310 Chirality : 0.038 0.236 4653 Planarity : 0.004 0.042 4165 Dihedral : 25.880 179.971 6658 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.54 % Allowed : 22.95 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.96 (0.17), residues: 2640 helix: 1.51 (0.14), residues: 1461 sheet: -0.67 (0.44), residues: 128 loop : -0.38 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 261 HIS 0.007 0.001 HIS E 39 PHE 0.025 0.001 PHE M 17 TYR 0.021 0.002 TYR M 373 ARG 0.007 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7974.08 seconds wall clock time: 143 minutes 11.58 seconds (8591.58 seconds total)