Starting phenix.real_space_refine on Tue Mar 12 00:39:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy7_27777/03_2024/8dy7_27777_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy7_27777/03_2024/8dy7_27777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy7_27777/03_2024/8dy7_27777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy7_27777/03_2024/8dy7_27777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy7_27777/03_2024/8dy7_27777_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dy7_27777/03_2024/8dy7_27777_updated.pdb" } resolution = 3.18 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= 1.010 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: 9 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 3 6.06 5 P 148 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 19061 2.51 5 N 5576 2.21 5 O 6267 1.98 5 H 29915 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 15": "OD1" <-> "OD2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "C GLU 400": "OE1" <-> "OE2" Residue "C GLU 432": "OE1" <-> "OE2" Residue "C ASP 650": "OD1" <-> "OD2" Residue "C ASP 736": "OD1" <-> "OD2" Residue "C ASP 803": "OD1" <-> "OD2" Residue "C GLU 821": "OE1" <-> "OE2" Residue "C GLU 1116": "OE1" <-> "OE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 749": "OE1" <-> "OE2" Residue "D TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 883": "OE1" <-> "OE2" Residue "D GLU 987": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "F GLU 245": "OE1" <-> "OE2" Residue "F TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 430": "OE1" <-> "OE2" Residue "F PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "I ASP 93": "OD1" <-> "OD2" 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: 61085 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3519 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 211} Chain: "B" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3671 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 221} Chain: "C" Number of atoms: 17368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 17368 Classifications: {'peptide': 1118} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1060} Chain: "D" Number of atoms: 19789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1253, 19789 Classifications: {'peptide': 1253} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1199} Chain breaks: 1 Chain: "E" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1202 Classifications: {'peptide': 77} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4857 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain: "G" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1647 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "H" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1208 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 82} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3187 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 205} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "O" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 2365 Classifications: {'DNA': 78} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 77} Chain breaks: 1 Chain: "P" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 2260 Classifications: {'DNA': 71} Link IDs: {'rna3p': 70} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 38735 SG CYS D 886 18.428 115.050 92.457 1.00 29.21 S ATOM 39874 SG CYS D 962 22.070 114.976 93.758 1.00 26.36 S ATOM 39957 SG CYS D 969 21.080 113.128 90.515 1.00 19.10 S ATOM 39997 SG CYS D 972 21.296 116.740 90.534 1.00 22.12 S ATOM 25506 SG CYS D 60 54.180 63.516 120.474 1.00 46.44 S ATOM 25537 SG CYS D 62 56.064 62.211 123.393 1.00 51.42 S ATOM 25770 SG CYS D 75 52.264 62.266 123.577 1.00 56.90 S ATOM 25819 SG CYS D 78 54.187 65.501 123.774 1.00 55.22 S ATOM 52313 SG CYS H 25 59.811 44.995 77.495 1.00 81.13 S ATOM 52653 SG CYS H 48 61.897 39.446 75.618 1.00 88.25 S ATOM 52783 SG CYS H 57 65.543 42.749 79.833 1.00 94.87 S ATOM 52692 SG CYS H 51 64.911 44.772 73.680 1.00 87.70 S ATOM 53538 SG CYS I 18 41.409 59.095 77.225 1.00 70.00 S ATOM 53548 SG CYS I 19 38.833 57.068 75.327 1.00 78.50 S ATOM 55071 SG CYS I 122 39.243 55.563 78.029 1.00 85.60 S Time building chain proxies: 19.42, per 1000 atoms: 0.32 Number of scatterers: 61085 At special positions: 0 Unit cell: (129.96, 173.28, 202.521, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 3 29.99 Fe 4 26.01 S 110 16.00 P 148 15.00 Mg 1 11.99 O 6267 8.00 N 5576 7.00 C 19061 6.00 H 29915 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.84 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 H 101 " pdb="FE2 SF4 H 101 " - pdb=" SG CYS H 48 " pdb="FE4 SF4 H 101 " - pdb=" SG CYS H 51 " pdb="FE1 SF4 H 101 " - pdb=" SG CYS H 25 " pdb="FE3 SF4 H 101 " - pdb=" SG CYS H 57 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 972 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 969 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 886 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 962 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 122 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 18 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 19 " Number of angles added : 12 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6652 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 31 sheets defined 37.2% alpha, 10.9% beta 61 base pairs and 108 stacking pairs defined. Time for finding SS restraints: 26.51 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.656A pdb=" N LEU A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 204 through 225 removed outlier: 3.839A pdb=" N GLU A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 44 Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 204 through 225 removed outlier: 3.836A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 66 removed outlier: 4.256A pdb=" N SER C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 78 Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 124 through 130 Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 250 through 256 Processing helix chain 'C' and resid 262 through 268 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 315 through 325 Processing helix chain 'C' and resid 338 through 353 Processing helix chain 'C' and resid 384 through 409 removed outlier: 3.654A pdb=" N ARG C 398 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR C 408 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 448 through 454 Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 594 through 596 No H-bonds generated for 'chain 'C' and resid 594 through 596' Processing helix chain 'C' and resid 605 through 614 Processing helix chain 'C' and resid 634 through 641 Processing helix chain 'C' and resid 743 through 746 No H-bonds generated for 'chain 'C' and resid 743 through 746' Processing helix chain 'C' and resid 819 through 828 Processing helix chain 'C' and resid 858 through 860 No H-bonds generated for 'chain 'C' and resid 858 through 860' Processing helix chain 'C' and resid 922 through 928 Proline residue: C 926 - end of helix Processing helix chain 'C' and resid 932 through 945 Processing helix chain 'C' and resid 955 through 962 removed outlier: 3.794A pdb=" N ARG C 959 " --> pdb=" O GLU C 955 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 960 " --> pdb=" O TRP C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 992 removed outlier: 4.235A pdb=" N ASN C 992 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1041 No H-bonds generated for 'chain 'C' and resid 1039 through 1041' Processing helix chain 'C' and resid 1072 through 1081 Processing helix chain 'C' and resid 1085 through 1092 Processing helix chain 'C' and resid 1098 through 1110 removed outlier: 4.453A pdb=" N VAL C1102 " --> pdb=" O VAL C1098 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS C1103 " --> pdb=" O THR C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1133 removed outlier: 3.669A pdb=" N LEU C1133 " --> pdb=" O GLU C1129 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 86 through 89 Processing helix chain 'D' and resid 104 through 108 removed outlier: 4.252A pdb=" N LYS D 108 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 183 Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 191 through 227 removed outlier: 4.927A pdb=" N VAL D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 248 Processing helix chain 'D' and resid 257 through 266 removed outlier: 3.684A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 Processing helix chain 'D' and resid 287 through 304 removed outlier: 3.827A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 340 through 360 removed outlier: 3.554A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 382 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 445 through 451 Processing helix chain 'D' and resid 453 through 462 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 482 through 490 removed outlier: 3.783A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 508 No H-bonds generated for 'chain 'D' and resid 506 through 508' Processing helix chain 'D' and resid 529 through 532 No H-bonds generated for 'chain 'D' and resid 529 through 532' Processing helix chain 'D' and resid 549 through 557 Processing helix chain 'D' and resid 561 through 563 No H-bonds generated for 'chain 'D' and resid 561 through 563' Processing helix chain 'D' and resid 582 through 588 Processing helix chain 'D' and resid 607 through 615 Processing helix chain 'D' and resid 663 through 670 removed outlier: 3.578A pdb=" N GLU D 670 " --> pdb=" O ALA D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 698 Processing helix chain 'D' and resid 701 through 720 Processing helix chain 'D' and resid 737 through 756 Processing helix chain 'D' and resid 762 through 787 Processing helix chain 'D' and resid 793 through 799 Processing helix chain 'D' and resid 806 through 812 Processing helix chain 'D' and resid 841 through 875 removed outlier: 3.945A pdb=" N HIS D 849 " --> pdb=" O PHE D 845 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA D 863 " --> pdb=" O ALA D 859 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY D 866 " --> pdb=" O THR D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 949 Processing helix chain 'D' and resid 959 through 961 No H-bonds generated for 'chain 'D' and resid 959 through 961' Processing helix chain 'D' and resid 970 through 973 No H-bonds generated for 'chain 'D' and resid 970 through 973' Processing helix chain 'D' and resid 989 through 1002 Proline residue: D1000 - end of helix Processing helix chain 'D' and resid 1023 through 1030 Processing helix chain 'D' and resid 1101 through 1128 removed outlier: 7.840A pdb=" N GLN D1110 " --> pdb=" O ARG D1106 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N ARG D1111 " --> pdb=" O ILE D1107 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA D1112 " --> pdb=" O LEU D1108 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL D1113 " --> pdb=" O GLY D1109 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D1124 " --> pdb=" O GLU D1120 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D1125 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN D1128 " --> pdb=" O VAL D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1143 removed outlier: 3.760A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1177 Processing helix chain 'D' and resid 1193 through 1198 Processing helix chain 'D' and resid 1203 through 1209 Processing helix chain 'D' and resid 1212 through 1222 removed outlier: 3.703A pdb=" N ILE D1221 " --> pdb=" O THR D1217 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN D1222 " --> pdb=" O ASP D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1231 through 1237 Processing helix chain 'D' and resid 1244 through 1246 No H-bonds generated for 'chain 'D' and resid 1244 through 1246' Processing helix chain 'D' and resid 1248 through 1251 No H-bonds generated for 'chain 'D' and resid 1248 through 1251' Processing helix chain 'D' and resid 1259 through 1264 Processing helix chain 'E' and resid 16 through 22 removed outlier: 3.811A pdb=" N ALA E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 45 removed outlier: 3.686A pdb=" N ILE E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 77 Processing helix chain 'F' and resid 218 through 228 removed outlier: 3.673A pdb=" N GLY F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS F 228 " --> pdb=" O LYS F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 Processing helix chain 'F' and resid 262 through 297 removed outlier: 4.706A pdb=" N ARG F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL F 290 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG F 296 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR F 297 " --> pdb=" O LEU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 321 Processing helix chain 'F' and resid 331 through 348 Processing helix chain 'F' and resid 357 through 377 Processing helix chain 'F' and resid 383 through 390 Processing helix chain 'F' and resid 394 through 404 removed outlier: 3.693A pdb=" N GLY F 404 " --> pdb=" O VAL F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 425 removed outlier: 3.717A pdb=" N LEU F 425 " --> pdb=" O PHE F 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 422 through 425' Processing helix chain 'F' and resid 434 through 452 removed outlier: 3.686A pdb=" N HIS F 448 " --> pdb=" O GLN F 444 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 466 Processing helix chain 'F' and resid 476 through 483 removed outlier: 3.800A pdb=" N VAL F 482 " --> pdb=" O GLU F 478 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 501 Processing helix chain 'F' and resid 508 through 511 No H-bonds generated for 'chain 'F' and resid 508 through 511' Processing helix chain 'G' and resid 82 through 89 Processing helix chain 'G' and resid 92 through 107 Processing helix chain 'H' and resid 4 through 7 No H-bonds generated for 'chain 'H' and resid 4 through 7' Processing helix chain 'H' and resid 25 through 27 No H-bonds generated for 'chain 'H' and resid 25 through 27' Processing helix chain 'H' and resid 30 through 33 Processing helix chain 'H' and resid 43 through 50 removed outlier: 3.640A pdb=" N ALA H 50 " --> pdb=" O LYS H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 64 Processing helix chain 'H' and resid 76 through 84 Processing helix chain 'I' and resid 3 through 10 Processing helix chain 'I' and resid 17 through 30 Processing helix chain 'I' and resid 50 through 63 removed outlier: 4.079A pdb=" N ARG I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 99 Processing helix chain 'I' and resid 121 through 134 Processing helix chain 'I' and resid 154 through 167 removed outlier: 3.682A pdb=" N LEU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 197 Processing helix chain 'I' and resid 201 through 213 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.716A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.761A pdb=" N SER A 53 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= D, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.501A pdb=" N ARG B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 93 through 97 removed outlier: 3.888A pdb=" N SER B 53 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 103 through 106 Processing sheet with id= G, first strand: chain 'C' and resid 171 through 173 Processing sheet with id= H, first strand: chain 'C' and resid 183 through 186 Processing sheet with id= I, first strand: chain 'C' and resid 189 through 196 removed outlier: 3.575A pdb=" N PHE C 205 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 217 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 457 through 459 Processing sheet with id= K, first strand: chain 'C' and resid 517 through 520 Processing sheet with id= L, first strand: chain 'C' and resid 562 through 565 Processing sheet with id= M, first strand: chain 'C' and resid 670 through 674 removed outlier: 6.194A pdb=" N ALA C 664 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL C 653 " --> pdb=" O ALA C 664 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 1027 through 1033 removed outlier: 6.770A pdb=" N ILE C 918 " --> pdb=" O ALA C 725 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 809 through 811 Processing sheet with id= P, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= Q, first strand: chain 'C' and resid 108 through 117 removed outlier: 4.435A pdb=" N HIS C 115 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE C 139 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE C 117 " --> pdb=" O PRO C 137 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY C 160 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL C 140 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N PHE C 158 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA C 142 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR C 156 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 738 through 741 removed outlier: 7.390A pdb=" N LEU C 740 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE C 901 " --> pdb=" O LEU C 740 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 752 through 763 removed outlier: 3.753A pdb=" N GLY C 852 " --> pdb=" O TYR C 875 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA C 877 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE C 850 " --> pdb=" O ALA C 877 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 93 through 96 Processing sheet with id= U, first strand: chain 'D' and resid 425 through 429 Processing sheet with id= V, first strand: chain 'D' and resid 430 through 432 removed outlier: 6.193A pdb=" N ILE D 522 " --> pdb=" O VAL D 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 625 through 628 Processing sheet with id= X, first strand: chain 'D' and resid 892 through 895 Processing sheet with id= Y, first strand: chain 'D' and resid 1046 through 1053 Processing sheet with id= Z, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id= AA, first strand: chain 'D' and resid 135 through 139 removed outlier: 6.269A pdb=" N ASP D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 27 through 33 Processing sheet with id= AC, first strand: chain 'G' and resid 53 through 55 Processing sheet with id= AD, first strand: chain 'I' and resid 32 through 37 Processing sheet with id= AE, first strand: chain 'I' and resid 149 through 151 removed outlier: 4.430A pdb=" N ASP I 180 " --> pdb=" O CYS I 151 " (cutoff:3.500A) 1025 hydrogen bonds defined for protein. 2976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 163 hydrogen bonds 326 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 108 stacking parallelities Total time for adding SS restraints: 23.09 Time building geometry restraints manager: 38.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 29903 1.13 - 1.41: 12782 1.41 - 1.70: 19017 1.70 - 1.99: 185 1.99 - 2.28: 12 Bond restraints: 61899 Sorted by residual: bond pdb=" C3' DG P 48 " pdb=" O3' DG P 48 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.77e+00 bond pdb=" N MET I 1 " pdb=" CA MET I 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" C3' DC O 64 " pdb=" O3' DC O 64 " ideal model delta sigma weight residual 1.422 1.469 -0.047 3.00e-02 1.11e+03 2.48e+00 bond pdb=" N MET I 1 " pdb=" H MET I 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C VAL C 85 " pdb=" N PRO C 86 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.21e+00 ... (remaining 61894 not shown) Histogram of bond angle deviations from ideal: 73.05 - 85.58: 15 85.58 - 98.10: 1 98.10 - 110.63: 65038 110.63 - 123.16: 41142 123.16 - 135.68: 6030 Bond angle restraints: 112226 Sorted by residual: angle pdb=" OP1 DG P 49 " pdb=" P DG P 49 " pdb=" OP2 DG P 49 " ideal model delta sigma weight residual 120.00 79.65 40.35 3.00e+00 1.11e-01 1.81e+02 angle pdb=" O3' DG P 48 " pdb=" P DG P 49 " pdb=" OP2 DG P 49 " ideal model delta sigma weight residual 108.00 73.05 34.95 3.00e+00 1.11e-01 1.36e+02 angle pdb=" OP1 DG P 49 " pdb=" P DG P 49 " pdb=" O5' DG P 49 " ideal model delta sigma weight residual 109.00 76.76 32.24 3.00e+00 1.11e-01 1.15e+02 angle pdb=" OP2 DG P 49 " pdb=" P DG P 49 " pdb=" O5' DG P 49 " ideal model delta sigma weight residual 108.00 135.68 -27.68 3.00e+00 1.11e-01 8.51e+01 angle pdb=" O3' DG P 48 " pdb=" P DG P 49 " pdb=" OP1 DG P 49 " ideal model delta sigma weight residual 108.00 133.84 -25.84 3.00e+00 1.11e-01 7.42e+01 ... (remaining 112221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 26918 35.19 - 70.38: 1187 70.38 - 105.57: 34 105.57 - 140.76: 0 140.76 - 175.95: 9 Dihedral angle restraints: 28148 sinusoidal: 16672 harmonic: 11476 Sorted by residual: dihedral pdb=" CA PRO D 641 " pdb=" C PRO D 641 " pdb=" N PRO D 642 " pdb=" CA PRO D 642 " ideal model delta harmonic sigma weight residual 180.00 144.85 35.15 0 5.00e+00 4.00e-02 4.94e+01 dihedral pdb=" CA SER A 44 " pdb=" C SER A 44 " pdb=" N SER A 45 " pdb=" CA SER A 45 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA VAL A 147 " pdb=" C VAL A 147 " pdb=" N SER A 148 " pdb=" CA SER A 148 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 28145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4228 0.055 - 0.110: 648 0.110 - 0.165: 111 0.165 - 0.220: 0 0.220 - 0.275: 1 Chirality restraints: 4988 Sorted by residual: chirality pdb=" P DG P 49 " pdb=" OP1 DG P 49 " pdb=" OP2 DG P 49 " pdb=" O5' DG P 49 " both_signs ideal model delta sigma weight residual True 2.35 2.07 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE C 597 " pdb=" N ILE C 597 " pdb=" C ILE C 597 " pdb=" CB ILE C 597 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE D 509 " pdb=" N ILE D 509 " pdb=" C ILE D 509 " pdb=" CB ILE D 509 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 4985 not shown) Planarity restraints: 8774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C1142 " 0.029 2.00e-02 2.50e+03 5.72e-02 3.27e+01 pdb=" C SER C1142 " -0.099 2.00e-02 2.50e+03 pdb=" O SER C1142 " 0.037 2.00e-02 2.50e+03 pdb=" N ASP C1143 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 641 " -0.060 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO D 642 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO D 642 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 642 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 470 " 0.252 9.50e-02 1.11e+02 8.51e-02 1.17e+01 pdb=" NE ARG C 470 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 470 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG C 470 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG C 470 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG C 470 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG C 470 " 0.011 2.00e-02 2.50e+03 pdb="HH21 ARG C 470 " 0.008 2.00e-02 2.50e+03 pdb="HH22 ARG C 470 " -0.006 2.00e-02 2.50e+03 ... (remaining 8771 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1037 2.13 - 2.74: 107197 2.74 - 3.36: 164914 3.36 - 3.98: 211710 3.98 - 4.60: 334512 Nonbonded interactions: 819370 Sorted by model distance: nonbonded pdb=" OD1 ASP I 123 " pdb="ZN ZN I2000 " model vdw 1.507 2.110 nonbonded pdb=" OE2 GLU D 81 " pdb="HH22 ARG D 91 " model vdw 1.602 1.850 nonbonded pdb=" OD2 ASP C 444 " pdb=" HG SER C 450 " model vdw 1.633 1.850 nonbonded pdb=" OG1 THR B 41 " pdb=" HG SER B 45 " model vdw 1.645 1.850 nonbonded pdb=" OE1 GLU F 235 " pdb=" H GLU F 235 " model vdw 1.653 1.850 ... (remaining 819365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 3 through 226)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.690 Extract box with map and model: 7.770 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 187.160 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31984 Z= 0.201 Angle : 0.647 40.347 43894 Z= 0.323 Chirality : 0.041 0.275 4988 Planarity : 0.004 0.114 5234 Dihedral : 17.405 175.947 12494 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 0.22 (0.14), residues: 3592 helix: 1.75 (0.15), residues: 1375 sheet: -0.22 (0.25), residues: 411 loop : -1.07 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 773 HIS 0.007 0.001 HIS C 482 PHE 0.027 0.001 PHE C 376 TYR 0.040 0.001 TYR E 32 ARG 0.030 0.000 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 3.353 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: C 98 ILE cc_start: 0.7884 (tp) cc_final: 0.7500 (tp) REVERT: C 159 MET cc_start: 0.8306 (mmm) cc_final: 0.7997 (mmt) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.9159 time to fit residues: 526.8713 Evaluate side-chains 314 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 8.9990 chunk 281 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 336 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 933 GLN C 958 GLN ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1034 GLN H 27 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31984 Z= 0.333 Angle : 0.637 39.892 43894 Z= 0.317 Chirality : 0.042 0.244 4988 Planarity : 0.004 0.076 5234 Dihedral : 18.731 174.888 5534 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.50 % Allowed : 5.47 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3592 helix: 1.57 (0.14), residues: 1396 sheet: -0.20 (0.25), residues: 421 loop : -1.19 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 773 HIS 0.007 0.001 HIS D 505 PHE 0.023 0.002 PHE C 376 TYR 0.032 0.002 TYR E 32 ARG 0.005 0.000 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 344 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 329 time to evaluate : 3.398 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: C 159 MET cc_start: 0.8236 (mmm) cc_final: 0.7967 (mmt) REVERT: C 418 GLN cc_start: 0.7604 (mp10) cc_final: 0.7337 (mp10) REVERT: F 328 TYR cc_start: 0.6860 (m-80) cc_final: 0.6617 (m-80) REVERT: F 436 ASP cc_start: 0.7057 (m-30) cc_final: 0.6644 (m-30) outliers start: 15 outliers final: 11 residues processed: 335 average time/residue: 0.8836 time to fit residues: 454.3206 Evaluate side-chains 320 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 309 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 109 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 337 optimal weight: 9.9990 chunk 364 optimal weight: 20.0000 chunk 300 optimal weight: 4.9990 chunk 334 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 270 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1034 GLN E 62 HIS ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31984 Z= 0.289 Angle : 0.626 40.259 43894 Z= 0.310 Chirality : 0.041 0.213 4988 Planarity : 0.004 0.070 5234 Dihedral : 18.720 174.136 5534 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.56 % Allowed : 7.83 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3592 helix: 1.60 (0.14), residues: 1399 sheet: -0.07 (0.25), residues: 415 loop : -1.21 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.006 0.001 HIS D 505 PHE 0.021 0.001 PHE C 376 TYR 0.029 0.001 TYR E 32 ARG 0.003 0.000 ARG C1046 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 332 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 315 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8182 (mmm) cc_final: 0.7742 (mmt) REVERT: C 589 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7805 (ptt) outliers start: 17 outliers final: 14 residues processed: 322 average time/residue: 0.9062 time to fit residues: 447.5644 Evaluate side-chains 322 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 307 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain I residue 109 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 333 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 chunk 175 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 338 optimal weight: 5.9990 chunk 358 optimal weight: 20.0000 chunk 176 optimal weight: 8.9990 chunk 321 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1034 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31984 Z= 0.280 Angle : 0.620 40.071 43894 Z= 0.307 Chirality : 0.041 0.237 4988 Planarity : 0.004 0.066 5234 Dihedral : 18.700 173.962 5534 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.86 % Allowed : 8.73 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3592 helix: 1.62 (0.14), residues: 1399 sheet: -0.10 (0.25), residues: 419 loop : -1.22 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.005 0.001 HIS D 94 PHE 0.015 0.001 PHE C 144 TYR 0.023 0.001 TYR E 32 ARG 0.004 0.000 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 338 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 312 time to evaluate : 3.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8186 (mmm) cc_final: 0.7743 (mmt) REVERT: C 561 ARG cc_start: 0.6659 (ttt90) cc_final: 0.6451 (mtp85) REVERT: C 589 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7746 (ptt) REVERT: D 806 MET cc_start: 0.7421 (mmt) cc_final: 0.7102 (mmt) REVERT: D 1103 ASP cc_start: 0.6372 (m-30) cc_final: 0.6017 (m-30) outliers start: 26 outliers final: 23 residues processed: 327 average time/residue: 0.9187 time to fit residues: 459.0357 Evaluate side-chains 329 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 305 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 208 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 298 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN D1034 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 31984 Z= 0.386 Angle : 0.654 39.988 43894 Z= 0.327 Chirality : 0.043 0.253 4988 Planarity : 0.005 0.063 5234 Dihedral : 18.755 174.320 5534 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.09 % Allowed : 9.72 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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 (0.14), residues: 3592 helix: 1.43 (0.14), residues: 1395 sheet: -0.26 (0.25), residues: 420 loop : -1.31 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 773 HIS 0.007 0.001 HIS D 505 PHE 0.018 0.002 PHE D 452 TYR 0.025 0.002 TYR E 32 ARG 0.005 0.000 ARG C1046 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 309 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8153 (mmm) cc_final: 0.7672 (mmt) REVERT: C 561 ARG cc_start: 0.6712 (ttt90) cc_final: 0.6510 (mtp85) REVERT: C 589 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7731 (ptt) REVERT: C 1031 TYR cc_start: 0.8952 (t80) cc_final: 0.8626 (t80) REVERT: D 806 MET cc_start: 0.7477 (mmt) cc_final: 0.7149 (mmt) REVERT: D 1103 ASP cc_start: 0.6382 (m-30) cc_final: 0.6009 (m-30) REVERT: H 62 LEU cc_start: 0.8840 (tp) cc_final: 0.8626 (tt) outliers start: 33 outliers final: 25 residues processed: 329 average time/residue: 0.9093 time to fit residues: 459.4235 Evaluate side-chains 327 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 301 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 208 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 120 optimal weight: 4.9990 chunk 322 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 358 optimal weight: 20.0000 chunk 297 optimal weight: 3.9990 chunk 166 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 188 optimal weight: 0.0470 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 369 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1034 GLN F 309 GLN H 63 GLN ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31984 Z= 0.185 Angle : 0.599 40.183 43894 Z= 0.294 Chirality : 0.040 0.229 4988 Planarity : 0.004 0.066 5234 Dihedral : 18.690 173.708 5534 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.80 % Allowed : 10.29 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 0.23 (0.14), residues: 3592 helix: 1.78 (0.14), residues: 1394 sheet: -0.11 (0.25), residues: 399 loop : -1.14 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 773 HIS 0.004 0.001 HIS D 94 PHE 0.014 0.001 PHE C 144 TYR 0.016 0.001 TYR E 32 ARG 0.003 0.000 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 313 time to evaluate : 3.444 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: C 159 MET cc_start: 0.8099 (mmm) cc_final: 0.7632 (mmt) REVERT: D 749 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7576 (tm-30) REVERT: D 806 MET cc_start: 0.7401 (mmt) cc_final: 0.7085 (mmt) REVERT: D 1103 ASP cc_start: 0.6373 (m-30) cc_final: 0.6008 (m-30) REVERT: H 62 LEU cc_start: 0.8873 (tp) cc_final: 0.8623 (tt) outliers start: 24 outliers final: 21 residues processed: 324 average time/residue: 0.9066 time to fit residues: 451.9319 Evaluate side-chains 331 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 310 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 208 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 346 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 357 optimal weight: 20.0000 chunk 223 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1034 GLN E 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31984 Z= 0.166 Angle : 0.587 40.081 43894 Z= 0.286 Chirality : 0.040 0.243 4988 Planarity : 0.004 0.064 5234 Dihedral : 18.624 173.693 5534 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.80 % Allowed : 10.62 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 0.44 (0.14), residues: 3592 helix: 2.02 (0.14), residues: 1387 sheet: -0.16 (0.25), residues: 413 loop : -1.02 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 773 HIS 0.004 0.001 HIS D 94 PHE 0.016 0.001 PHE D 226 TYR 0.014 0.001 TYR E 32 ARG 0.003 0.000 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 321 time to evaluate : 3.462 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: C 159 MET cc_start: 0.8093 (mmm) cc_final: 0.7634 (mmt) REVERT: C 589 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7624 (ptt) REVERT: D 576 MET cc_start: 0.7927 (ttp) cc_final: 0.7705 (mtp) REVERT: D 806 MET cc_start: 0.7419 (mmt) cc_final: 0.7119 (mmt) REVERT: H 62 LEU cc_start: 0.8873 (tp) cc_final: 0.8628 (tt) outliers start: 24 outliers final: 19 residues processed: 331 average time/residue: 0.9061 time to fit residues: 460.5324 Evaluate side-chains 333 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 313 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 208 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 221 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 213 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 chunk 33 optimal weight: 0.2980 chunk 281 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1034 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31984 Z= 0.206 Angle : 0.595 40.073 43894 Z= 0.291 Chirality : 0.040 0.242 4988 Planarity : 0.004 0.061 5234 Dihedral : 18.618 173.744 5534 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.86 % Allowed : 10.82 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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 (0.14), residues: 3592 helix: 2.00 (0.14), residues: 1387 sheet: -0.15 (0.25), residues: 427 loop : -1.02 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.005 0.001 HIS D 94 PHE 0.015 0.001 PHE D 226 TYR 0.015 0.001 TYR E 32 ARG 0.003 0.000 ARG C1046 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 341 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 315 time to evaluate : 3.385 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 136 MET cc_start: 0.8800 (ttm) cc_final: 0.8537 (ttp) REVERT: C 159 MET cc_start: 0.8106 (mmm) cc_final: 0.7630 (mmt) REVERT: C 589 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7637 (ptt) REVERT: D 806 MET cc_start: 0.7431 (mmt) cc_final: 0.7127 (mmt) REVERT: H 62 LEU cc_start: 0.8865 (tp) cc_final: 0.8628 (tt) outliers start: 26 outliers final: 23 residues processed: 327 average time/residue: 0.8919 time to fit residues: 449.4265 Evaluate side-chains 337 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 313 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 208 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 325 optimal weight: 9.9990 chunk 342 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 333 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 301 optimal weight: 4.9990 chunk 315 optimal weight: 0.8980 chunk 332 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1034 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31984 Z= 0.235 Angle : 0.603 40.040 43894 Z= 0.295 Chirality : 0.041 0.248 4988 Planarity : 0.004 0.060 5234 Dihedral : 18.613 173.796 5534 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.83 % Allowed : 11.18 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 0.39 (0.14), residues: 3592 helix: 1.93 (0.14), residues: 1388 sheet: -0.04 (0.25), residues: 415 loop : -1.05 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 223 HIS 0.005 0.001 HIS D 94 PHE 0.016 0.001 PHE C 144 TYR 0.017 0.001 TYR E 32 ARG 0.003 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 340 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 315 time to evaluate : 3.384 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 133 LYS cc_start: 0.8463 (ptpp) cc_final: 0.8211 (ptpp) REVERT: C 159 MET cc_start: 0.8072 (mmm) cc_final: 0.7607 (mmt) REVERT: C 589 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7645 (ptt) REVERT: D 806 MET cc_start: 0.7443 (mmt) cc_final: 0.7141 (mmt) REVERT: D 1103 ASP cc_start: 0.6302 (m-30) cc_final: 0.5926 (m-30) REVERT: H 62 LEU cc_start: 0.8891 (tp) cc_final: 0.8628 (tt) REVERT: H 79 ARG cc_start: 0.7453 (mmm-85) cc_final: 0.7248 (mmm-85) outliers start: 25 outliers final: 22 residues processed: 327 average time/residue: 0.9137 time to fit residues: 458.7377 Evaluate side-chains 334 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 311 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 208 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 218 optimal weight: 1.9990 chunk 352 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 369 optimal weight: 10.0000 chunk 340 optimal weight: 2.9990 chunk 294 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1034 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 31984 Z= 0.336 Angle : 0.639 39.941 43894 Z= 0.316 Chirality : 0.042 0.261 4988 Planarity : 0.004 0.056 5234 Dihedral : 18.656 174.014 5534 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.83 % Allowed : 11.41 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3592 helix: 1.66 (0.14), residues: 1394 sheet: -0.10 (0.25), residues: 423 loop : -1.17 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 223 HIS 0.006 0.001 HIS D 94 PHE 0.017 0.002 PHE D 452 TYR 0.022 0.002 TYR E 32 ARG 0.004 0.000 ARG C1046 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 172 is missing expected H atoms. Skipping. Evaluate side-chains 336 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 311 time to evaluate : 3.921 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: C 159 MET cc_start: 0.8086 (mmm) cc_final: 0.7583 (mmt) REVERT: C 589 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7676 (ptt) REVERT: D 806 MET cc_start: 0.7459 (mmt) cc_final: 0.7132 (mmt) REVERT: D 1103 ASP cc_start: 0.6371 (m-30) cc_final: 0.5991 (m-30) REVERT: H 62 LEU cc_start: 0.8888 (tp) cc_final: 0.8630 (tt) outliers start: 25 outliers final: 23 residues processed: 323 average time/residue: 0.9067 time to fit residues: 447.7412 Evaluate side-chains 329 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 305 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 675 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 208 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 233 optimal weight: 3.9990 chunk 313 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 271 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 302 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1034 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.176935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125295 restraints weight = 96295.629| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.86 r_work: 0.2947 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 31984 Z= 0.160 Angle : 0.595 40.147 43894 Z= 0.290 Chirality : 0.040 0.236 4988 Planarity : 0.004 0.062 5234 Dihedral : 18.599 173.533 5534 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.66 % Allowed : 11.51 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 0.41 (0.14), residues: 3592 helix: 1.96 (0.14), residues: 1387 sheet: -0.04 (0.25), residues: 406 loop : -1.04 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 773 HIS 0.004 0.001 HIS D 94 PHE 0.016 0.001 PHE C 144 TYR 0.014 0.001 TYR E 32 ARG 0.006 0.000 ARG H 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10361.38 seconds wall clock time: 180 minutes 9.09 seconds (10809.09 seconds total)