Starting phenix.real_space_refine on Wed Apr 10 16:17:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9e_36984/04_2024/8k9e_36984_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9e_36984/04_2024/8k9e_36984.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9e_36984/04_2024/8k9e_36984_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9e_36984/04_2024/8k9e_36984_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9e_36984/04_2024/8k9e_36984_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9e_36984/04_2024/8k9e_36984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9e_36984/04_2024/8k9e_36984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9e_36984/04_2024/8k9e_36984_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9e_36984/04_2024/8k9e_36984_neut_updated.pdb" } resolution = 3.33 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= 0.015 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 Fe 21 7.16 5 P 2 5.49 5 S 115 5.16 5 C 13006 2.51 5 N 3302 2.21 5 O 3508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B GLU 655": "OE1" <-> "OE2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "B GLU 761": "OE1" <-> "OE2" Residue "B GLU 1025": "OE1" <-> "OE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F ARG 327": "NH1" <-> "NH2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "I GLU 4": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19954 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1763 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "B" Number of atoms: 7350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7350 Classifications: {'peptide': 951} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 892} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3655 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 23, 'TRANS': 425} Chain: "D" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1350 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 15, 'TRANS': 159} Chain: "E" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1292 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 153} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3128 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 20, 'TRANS': 376} Chain: "G" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 623 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 6, 'TRANS': 73} Chain: "I" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 305 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'HEC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 58 Unusual residues: {'EL6': 1, 'F3S': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'JLQ': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'EL6': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'JL3': 1, 'JM9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7333 SG CYS B 797 42.709 71.437 65.023 1.00 14.12 S ATOM 8689 SG CYS B 972 42.235 72.550 59.784 1.00 12.22 S ATOM 7352 SG CYS B 800 47.731 70.419 62.164 1.00 8.63 S ATOM 7315 SG CYS B 794 45.549 76.287 63.129 1.00 13.08 S ATOM 8420 SG CYS B 934 50.726 63.790 53.719 1.00 9.55 S ATOM 8395 SG CYS B 931 55.001 68.160 54.498 1.00 10.74 S ATOM 7377 SG CYS B 804 53.124 64.605 58.929 1.00 8.42 S ATOM 8660 SG CYS B 968 48.668 68.385 55.869 1.00 9.37 S ATOM 7749 SG CYS B 850 60.112 71.209 52.956 1.00 8.56 S ATOM 7808 SG CYS B 858 66.265 71.759 51.529 1.00 6.73 S ATOM 8067 SG CYS B 892 64.430 74.319 56.605 1.00 5.68 S ATOM 7772 SG CYS B 853 61.954 76.329 50.967 1.00 7.74 S ATOM 7837 SG CYS B 862 72.303 65.853 51.195 1.00 7.39 S ATOM 8039 SG CYS B 888 69.875 68.001 55.781 1.00 6.79 S ATOM 7994 SG CYS B 882 70.712 61.936 55.644 1.00 9.38 S Time building chain proxies: 10.90, per 1000 atoms: 0.55 Number of scatterers: 19954 At special positions: 0 Unit cell: (157.5, 133.35, 111.3, 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) Fe 21 26.01 S 115 16.00 P 2 15.00 O 3508 8.00 N 3302 7.00 C 13006 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=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.87 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B1104 " pdb="FE3 F3S B1104 " - pdb=" SG CYS B 888 " pdb="FE1 F3S B1104 " - pdb=" SG CYS B 862 " pdb="FE4 F3S B1104 " - pdb=" SG CYS B 882 " pdb=" SF4 B1101 " pdb="FE1 SF4 B1101 " - pdb=" SG CYS B 797 " pdb="FE4 SF4 B1101 " - pdb=" SG CYS B 794 " pdb="FE2 SF4 B1101 " - pdb=" SG CYS B 972 " pdb="FE3 SF4 B1101 " - pdb=" SG CYS B 800 " pdb=" SF4 B1102 " pdb="FE1 SF4 B1102 " - pdb=" SG CYS B 934 " pdb="FE2 SF4 B1102 " - pdb=" SG CYS B 931 " pdb="FE3 SF4 B1102 " - pdb=" SG CYS B 804 " pdb="FE4 SF4 B1102 " - pdb=" SG CYS B 968 " pdb=" SF4 B1103 " pdb="FE4 SF4 B1103 " - pdb=" SG CYS B 853 " pdb="FE1 SF4 B1103 " - pdb=" SG CYS B 850 " pdb="FE3 SF4 B1103 " - pdb=" SG CYS B 892 " pdb="FE2 SF4 B1103 " - pdb=" SG CYS B 858 " Number of angles added : 45 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4564 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 11 sheets defined 49.2% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 7 through 35 removed outlier: 3.839A pdb=" N ASN A 10 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 41 No H-bonds generated for 'chain 'A' and resid 38 through 41' Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 84 through 91 removed outlier: 4.427A pdb=" N CYS A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 106 removed outlier: 3.617A pdb=" N GLU A 102 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS A 103 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.596A pdb=" N CYS A 167 " --> pdb=" O TRP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 192 through 203 Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 214 through 217 No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'B' and resid 142 through 151 removed outlier: 3.529A pdb=" N GLU B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 149 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'B' and resid 201 through 213 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 268 through 279 Processing helix chain 'B' and resid 300 through 303 No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 314 through 327 removed outlier: 3.649A pdb=" N ALA B 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'B' and resid 401 through 414 Processing helix chain 'B' and resid 427 through 430 No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 433 through 435 No H-bonds generated for 'chain 'B' and resid 433 through 435' Processing helix chain 'B' and resid 437 through 443 removed outlier: 3.921A pdb=" N SER B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 459 No H-bonds generated for 'chain 'B' and resid 456 through 459' Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 528 through 537 Processing helix chain 'B' and resid 555 through 559 Processing helix chain 'B' and resid 584 through 586 No H-bonds generated for 'chain 'B' and resid 584 through 586' Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 611 through 618 Processing helix chain 'B' and resid 631 through 644 removed outlier: 5.038A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 751 through 762 removed outlier: 4.400A pdb=" N ILE B 754 " --> pdb=" O PRO B 751 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL B 758 " --> pdb=" O ALA B 755 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR B 759 " --> pdb=" O LYS B 756 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN B 760 " --> pdb=" O GLU B 757 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 762 " --> pdb=" O TYR B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 808 Processing helix chain 'B' and resid 815 through 819 Processing helix chain 'B' and resid 857 through 860 No H-bonds generated for 'chain 'B' and resid 857 through 860' Processing helix chain 'B' and resid 887 through 891 Processing helix chain 'B' and resid 910 through 915 Processing helix chain 'B' and resid 935 through 952 Processing helix chain 'B' and resid 967 through 971 Processing helix chain 'B' and resid 988 through 993 Processing helix chain 'B' and resid 1022 through 1025 No H-bonds generated for 'chain 'B' and resid 1022 through 1025' Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.875A pdb=" N VAL C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 42 No H-bonds generated for 'chain 'C' and resid 40 through 42' Processing helix chain 'C' and resid 45 through 71 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 86 through 111 removed outlier: 3.719A pdb=" N GLY C 98 " --> pdb=" O TRP C 94 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY C 101 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.902A pdb=" N LEU C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Proline residue: C 138 - end of helix removed outlier: 4.064A pdb=" N LEU C 142 " --> pdb=" O PRO C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 removed outlier: 4.863A pdb=" N TYR C 149 " --> pdb=" O TRP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 199 Proline residue: C 192 - end of helix Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 224 through 255 Proline residue: C 240 - end of helix removed outlier: 5.077A pdb=" N PHE C 253 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 292 Proline residue: C 267 - end of helix removed outlier: 3.549A pdb=" N PHE C 279 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 286 " --> pdb=" O LEU C 283 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE C 287 " --> pdb=" O LEU C 284 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.504A pdb=" N PHE C 292 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 331 Processing helix chain 'C' and resid 335 through 346 Processing helix chain 'C' and resid 350 through 360 Processing helix chain 'C' and resid 362 through 368 Proline residue: C 366 - end of helix No H-bonds generated for 'chain 'C' and resid 362 through 368' Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 376 through 403 removed outlier: 3.709A pdb=" N ILE C 400 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 418 through 441 Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'D' and resid 15 through 24 Processing helix chain 'D' and resid 44 through 48 Processing helix chain 'D' and resid 55 through 79 Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 100 through 122 Processing helix chain 'D' and resid 136 through 142 removed outlier: 4.191A pdb=" N GLN D 139 " --> pdb=" O PRO D 136 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER D 142 " --> pdb=" O GLN D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 168 Processing helix chain 'E' and resid 68 through 71 No H-bonds generated for 'chain 'E' and resid 68 through 71' Processing helix chain 'E' and resid 89 through 101 Processing helix chain 'E' and resid 116 through 119 No H-bonds generated for 'chain 'E' and resid 116 through 119' Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 138 through 146 Processing helix chain 'E' and resid 171 through 188 removed outlier: 3.568A pdb=" N GLN E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 40 through 70 removed outlier: 3.890A pdb=" N THR F 56 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) Proline residue: F 58 - end of helix Processing helix chain 'F' and resid 74 through 104 removed outlier: 4.928A pdb=" N ARG F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N MET F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR F 89 " --> pdb=" O ALA F 85 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU F 90 " --> pdb=" O GLY F 86 " (cutoff:3.500A) Proline residue: F 91 - end of helix removed outlier: 3.856A pdb=" N ILE F 98 " --> pdb=" O GLY F 94 " (cutoff:3.500A) Proline residue: F 99 - end of helix Processing helix chain 'F' and resid 123 through 126 No H-bonds generated for 'chain 'F' and resid 123 through 126' Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 146 through 176 removed outlier: 3.575A pdb=" N ASP F 175 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA F 176 " --> pdb=" O ARG F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 209 removed outlier: 3.874A pdb=" N ALA F 196 " --> pdb=" O GLY F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing helix chain 'F' and resid 224 through 244 Processing helix chain 'F' and resid 257 through 287 Processing helix chain 'F' and resid 291 through 301 Proline residue: F 295 - end of helix Processing helix chain 'F' and resid 305 through 314 Processing helix chain 'F' and resid 318 through 325 Processing helix chain 'F' and resid 333 through 358 Proline residue: F 357 - end of helix Processing helix chain 'F' and resid 363 through 365 No H-bonds generated for 'chain 'F' and resid 363 through 365' Processing helix chain 'F' and resid 368 through 391 Proline residue: F 374 - end of helix removed outlier: 3.744A pdb=" N GLN F 390 " --> pdb=" O ALA F 386 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 405 No H-bonds generated for 'chain 'F' and resid 402 through 405' Processing helix chain 'G' and resid 33 through 54 Processing helix chain 'G' and resid 71 through 80 Processing helix chain 'G' and resid 99 through 106 Processing helix chain 'I' and resid 10 through 34 Processing sheet with id= A, first strand: chain 'B' and resid 100 through 107 removed outlier: 3.710A pdb=" N LYS B 126 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 191 through 194 removed outlier: 6.475A pdb=" N THR B 419 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU B 194 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 421 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 446 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N MET B 422 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE B 448 " --> pdb=" O MET B 422 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 242 through 246 Processing sheet with id= D, first strand: chain 'B' and resid 358 through 362 removed outlier: 6.664A pdb=" N VAL B 253 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE B 361 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 255 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG B 290 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N SER B 256 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR B 292 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N HIS B 307 " --> pdb=" O VAL B 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 475 through 477 Processing sheet with id= F, first strand: chain 'B' and resid 571 through 576 Processing sheet with id= G, first strand: chain 'B' and resid 607 through 609 Processing sheet with id= H, first strand: chain 'B' and resid 741 through 743 removed outlier: 6.522A pdb=" N ARG B1016 " --> pdb=" O GLY B 742 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 977 through 981 removed outlier: 6.608A pdb=" N THR B1012 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 828 through 831 Processing sheet with id= K, first strand: chain 'D' and resid 175 through 177 784 hydrogen bonds defined for protein. 2115 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.31 Time building geometry restraints manager: 9.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.71: 20316 1.71 - 2.25: 193 2.25 - 2.79: 38 2.79 - 3.33: 0 3.33 - 3.87: 3 Bond restraints: 20550 Sorted by residual: bond pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " ideal model delta sigma weight residual 2.258 3.867 -1.609 2.00e-02 2.50e+03 6.48e+03 bond pdb=" S4 F3S B1104 " pdb="FE1 F3S B1104 " ideal model delta sigma weight residual 2.233 3.778 -1.545 2.00e-02 2.50e+03 5.97e+03 bond pdb=" S2 F3S B1104 " pdb="FE3 F3S B1104 " ideal model delta sigma weight residual 2.300 3.677 -1.377 2.00e-02 2.50e+03 4.74e+03 bond pdb=" CE1 HIS E 107 " pdb=" NE2 HIS E 107 " ideal model delta sigma weight residual 1.321 1.395 -0.074 1.00e-02 1.00e+04 5.42e+01 bond pdb=" C VAL I 30 " pdb=" O VAL I 30 " ideal model delta sigma weight residual 1.237 1.174 0.062 1.13e-02 7.83e+03 3.05e+01 ... (remaining 20545 not shown) Histogram of bond angle deviations from ideal: 36.95 - 65.55: 5 65.55 - 94.15: 68 94.15 - 122.75: 25209 122.75 - 151.36: 2805 151.36 - 179.96: 12 Bond angle restraints: 28099 Sorted by residual: angle pdb=" S3 F3S B1104 " pdb="FE1 F3S B1104 " pdb=" S4 F3S B1104 " ideal model delta sigma weight residual 112.59 66.54 46.05 3.00e+00 1.11e-01 2.36e+02 angle pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " pdb=" S3 F3S B1104 " ideal model delta sigma weight residual 114.75 69.62 45.13 3.00e+00 1.11e-01 2.26e+02 angle pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " pdb=" S2 F3S B1104 " ideal model delta sigma weight residual 103.63 65.13 38.50 3.00e+00 1.11e-01 1.65e+02 angle pdb="FE1 F3S B1104 " pdb=" S4 F3S B1104 " pdb="FE3 F3S B1104 " ideal model delta sigma weight residual 74.86 36.95 37.91 3.00e+00 1.11e-01 1.60e+02 angle pdb=" S1 F3S B1104 " pdb="FE3 F3S B1104 " pdb=" S2 F3S B1104 " ideal model delta sigma weight residual 103.25 69.10 34.15 3.00e+00 1.11e-01 1.30e+02 ... (remaining 28094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 11587 35.26 - 70.52: 251 70.52 - 105.77: 33 105.77 - 141.03: 6 141.03 - 176.29: 5 Dihedral angle restraints: 11882 sinusoidal: 4744 harmonic: 7138 Sorted by residual: dihedral pdb=" C ASP D 144 " pdb=" N ASP D 144 " pdb=" CA ASP D 144 " pdb=" CB ASP D 144 " ideal model delta harmonic sigma weight residual -122.60 -140.58 17.98 0 2.50e+00 1.60e-01 5.17e+01 dihedral pdb=" N ASP D 144 " pdb=" C ASP D 144 " pdb=" CA ASP D 144 " pdb=" CB ASP D 144 " ideal model delta harmonic sigma weight residual 122.80 139.93 -17.13 0 2.50e+00 1.60e-01 4.70e+01 dihedral pdb=" C2C HEC A 301 " pdb=" C3C HEC A 301 " pdb=" CAC HEC A 301 " pdb=" CBC HEC A 301 " ideal model delta sinusoidal sigma weight residual 60.00 -15.50 75.50 2 1.00e+01 1.00e-02 4.50e+01 ... (remaining 11879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.569: 3045 3.569 - 7.139: 0 7.139 - 10.708: 0 10.708 - 14.277: 0 14.277 - 17.846: 1 Chirality restraints: 3046 Sorted by residual: chirality pdb=" S2 F3S B1104 " pdb="FE1 F3S B1104 " pdb="FE3 F3S B1104 " pdb="FE4 F3S B1104 " both_signs ideal model delta sigma weight residual False 10.77 -7.08 17.85 2.00e-01 2.50e+01 7.96e+03 chirality pdb=" C20 JLQ C 501 " pdb=" C19 JLQ C 501 " pdb=" C21 JLQ C 501 " pdb=" O30 JLQ C 501 " both_signs ideal model delta sigma weight residual False 2.51 0.89 1.62 2.00e-01 2.50e+01 6.59e+01 chirality pdb=" CA HIS E 27 " pdb=" N HIS E 27 " pdb=" C HIS E 27 " pdb=" CB HIS E 27 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 3043 not shown) Planarity restraints: 3540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC E 301 " -0.020 2.00e-02 2.50e+03 6.57e-02 9.72e+01 pdb=" C2C HEC E 301 " 0.180 2.00e-02 2.50e+03 pdb=" C3C HEC E 301 " -0.027 2.00e-02 2.50e+03 pdb=" C4C HEC E 301 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC E 301 " -0.035 2.00e-02 2.50e+03 pdb=" CHC HEC E 301 " -0.034 2.00e-02 2.50e+03 pdb=" CHD HEC E 301 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC E 301 " -0.053 2.00e-02 2.50e+03 pdb=" NC HEC E 301 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 301 " -0.023 2.00e-02 2.50e+03 6.48e-02 9.44e+01 pdb=" C2C HEC A 301 " 0.177 2.00e-02 2.50e+03 pdb=" C3C HEC A 301 " -0.036 2.00e-02 2.50e+03 pdb=" C4C HEC A 301 " -0.011 2.00e-02 2.50e+03 pdb=" CAC HEC A 301 " -0.026 2.00e-02 2.50e+03 pdb=" CHC HEC A 301 " -0.032 2.00e-02 2.50e+03 pdb=" CHD HEC A 301 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC A 301 " -0.052 2.00e-02 2.50e+03 pdb=" NC HEC A 301 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 302 " 0.020 2.00e-02 2.50e+03 5.93e-02 7.90e+01 pdb=" C2C HEC A 302 " -0.162 2.00e-02 2.50e+03 pdb=" C3C HEC A 302 " 0.024 2.00e-02 2.50e+03 pdb=" C4C HEC A 302 " 0.008 2.00e-02 2.50e+03 pdb=" CAC HEC A 302 " 0.030 2.00e-02 2.50e+03 pdb=" CHC HEC A 302 " 0.028 2.00e-02 2.50e+03 pdb=" CHD HEC A 302 " -0.005 2.00e-02 2.50e+03 pdb=" CMC HEC A 302 " 0.049 2.00e-02 2.50e+03 pdb=" NC HEC A 302 " 0.009 2.00e-02 2.50e+03 ... (remaining 3537 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 77 2.58 - 3.16: 16276 3.16 - 3.74: 31849 3.74 - 4.32: 46226 4.32 - 4.90: 75024 Nonbonded interactions: 169452 Sorted by model distance: nonbonded pdb=" NE2 HIS A 133 " pdb="FE HEC A 302 " model vdw 1.998 3.080 nonbonded pdb=" NE2 HIS A 218 " pdb="FE HEC A 301 " model vdw 2.001 3.080 nonbonded pdb=" NE2 HIS A 58 " pdb="FE HEC A 305 " model vdw 2.001 3.080 nonbonded pdb=" NE2 HIS A 55 " pdb="FE HEC A 304 " model vdw 2.002 3.080 nonbonded pdb=" SD MET E 162 " pdb="FE HEC E 301 " model vdw 2.004 3.360 ... (remaining 169447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 2.940 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 57.450 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.090 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.022 1.609 20550 Z= 1.531 Angle : 1.562 46.046 28099 Z= 1.041 Chirality : 0.338 17.846 3046 Planarity : 0.006 0.081 3540 Dihedral : 15.765 176.289 7318 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 1.91 % Allowed : 4.94 % Favored : 93.15 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.17), residues: 2455 helix: 2.47 (0.15), residues: 1218 sheet: 0.49 (0.46), residues: 155 loop : -1.11 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 296 HIS 0.054 0.003 HIS E 107 PHE 0.017 0.002 PHE C 276 TYR 0.036 0.002 TYR I 36 ARG 0.007 0.001 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 297 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 258 ASP cc_start: 0.6292 (t0) cc_final: 0.5960 (t0) REVERT: B 753 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8564 (p90) REVERT: C 444 MET cc_start: 0.7919 (ptp) cc_final: 0.7677 (mtm) REVERT: E 27 HIS cc_start: 0.8730 (OUTLIER) cc_final: 0.8110 (p90) REVERT: E 94 ARG cc_start: 0.7675 (tpt170) cc_final: 0.7359 (ttm-80) REVERT: E 162 MET cc_start: 0.8562 (tpt) cc_final: 0.7883 (tpt) outliers start: 39 outliers final: 13 residues processed: 329 average time/residue: 0.3477 time to fit residues: 173.1988 Evaluate side-chains 215 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 853 CYS Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 27 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 20.0000 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 115 optimal weight: 0.0970 chunk 141 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN B 145 GLN B 693 ASN C 463 GLN D 123 ASN D 139 GLN E 27 HIS ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 20550 Z= 0.268 Angle : 0.892 84.141 28099 Z= 0.358 Chirality : 0.051 1.469 3046 Planarity : 0.005 0.052 3540 Dihedral : 13.472 179.437 2936 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 1.71 % Allowed : 9.44 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2455 helix: 1.66 (0.15), residues: 1224 sheet: -0.12 (0.40), residues: 204 loop : -1.09 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 296 HIS 0.007 0.001 HIS E 107 PHE 0.016 0.002 PHE C 336 TYR 0.019 0.001 TYR C 269 ARG 0.005 0.001 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 218 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7939 (mpp) cc_final: 0.7614 (mpp) REVERT: B 258 ASP cc_start: 0.6645 (t0) cc_final: 0.6186 (t0) REVERT: B 928 MET cc_start: 0.9077 (tpp) cc_final: 0.8862 (tpp) REVERT: C 425 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8597 (mt) REVERT: C 444 MET cc_start: 0.8017 (ptp) cc_final: 0.7766 (mtm) REVERT: D 154 ASP cc_start: 0.8525 (t0) cc_final: 0.8180 (t70) REVERT: E 71 TYR cc_start: 0.8251 (m-80) cc_final: 0.8031 (m-80) REVERT: E 74 LEU cc_start: 0.7662 (mp) cc_final: 0.7372 (mt) REVERT: E 94 ARG cc_start: 0.7705 (tpt170) cc_final: 0.7373 (ttm-80) REVERT: E 107 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.7697 (t-90) REVERT: F 66 MET cc_start: 0.8764 (mtm) cc_final: 0.8389 (mtp) REVERT: F 187 MET cc_start: 0.7837 (mtp) cc_final: 0.7621 (mtm) outliers start: 35 outliers final: 28 residues processed: 244 average time/residue: 0.3729 time to fit residues: 137.2377 Evaluate side-chains 235 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 221 optimal weight: 0.9980 chunk 238 optimal weight: 20.0000 chunk 196 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN D 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 20550 Z= 0.270 Angle : 0.833 82.393 28099 Z= 0.342 Chirality : 0.052 1.619 3046 Planarity : 0.005 0.053 3540 Dihedral : 12.544 153.214 2925 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 2.35 % Allowed : 11.20 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2455 helix: 1.32 (0.15), residues: 1226 sheet: -0.12 (0.40), residues: 195 loop : -1.12 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 286 HIS 0.009 0.001 HIS E 107 PHE 0.017 0.002 PHE C 336 TYR 0.017 0.001 TYR A 34 ARG 0.005 0.000 ARG E 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 210 time to evaluate : 2.071 Fit side-chains revert: symmetry clash REVERT: B 184 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7333 (mtm180) REVERT: B 258 ASP cc_start: 0.6640 (t0) cc_final: 0.6091 (t0) REVERT: C 425 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8605 (mt) REVERT: E 74 LEU cc_start: 0.7690 (mp) cc_final: 0.7378 (mt) REVERT: E 94 ARG cc_start: 0.7652 (tpt170) cc_final: 0.7331 (ttm-80) REVERT: F 187 MET cc_start: 0.7849 (mtp) cc_final: 0.7648 (mtm) outliers start: 48 outliers final: 37 residues processed: 242 average time/residue: 0.3504 time to fit residues: 127.6187 Evaluate side-chains 236 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 198 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain I residue 29 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 105 optimal weight: 0.0970 chunk 148 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 234 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 20550 Z= 0.226 Angle : 0.807 81.930 28099 Z= 0.326 Chirality : 0.050 1.541 3046 Planarity : 0.005 0.053 3540 Dihedral : 11.943 142.999 2924 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.20 % Allowed : 12.03 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2455 helix: 1.27 (0.15), residues: 1229 sheet: -0.41 (0.39), residues: 205 loop : -1.13 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 286 HIS 0.005 0.001 HIS E 129 PHE 0.014 0.001 PHE C 336 TYR 0.014 0.001 TYR C 269 ARG 0.004 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 2.253 Fit side-chains REVERT: B 184 ARG cc_start: 0.7463 (ttm110) cc_final: 0.7245 (mtm180) REVERT: B 212 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7270 (mm-40) REVERT: B 258 ASP cc_start: 0.6482 (t0) cc_final: 0.5929 (t0) REVERT: B 829 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8425 (mp) REVERT: B 837 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7102 (t0) REVERT: C 425 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8608 (mt) REVERT: E 74 LEU cc_start: 0.7688 (mp) cc_final: 0.7410 (mt) REVERT: E 162 MET cc_start: 0.8005 (tpt) cc_final: 0.7668 (tpt) outliers start: 45 outliers final: 34 residues processed: 235 average time/residue: 0.3517 time to fit residues: 125.4914 Evaluate side-chains 227 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 829 ILE Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 448 PHE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 101 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 225 HIS F 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 20550 Z= 0.354 Angle : 0.864 81.998 28099 Z= 0.358 Chirality : 0.053 1.568 3046 Planarity : 0.005 0.056 3540 Dihedral : 11.841 142.888 2923 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.93 % Allowed : 12.03 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2455 helix: 0.99 (0.15), residues: 1232 sheet: -0.40 (0.39), residues: 195 loop : -1.29 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 286 HIS 0.006 0.002 HIS E 107 PHE 0.018 0.002 PHE C 336 TYR 0.025 0.002 TYR C 269 ARG 0.006 0.001 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 194 time to evaluate : 2.363 Fit side-chains revert: symmetry clash REVERT: B 184 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7442 (mtm180) REVERT: B 212 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7290 (mm-40) REVERT: B 258 ASP cc_start: 0.6421 (t0) cc_final: 0.5833 (t0) REVERT: B 555 GLU cc_start: 0.6431 (mm-30) cc_final: 0.6231 (mp0) REVERT: B 837 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7345 (t0) REVERT: C 425 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8665 (mt) REVERT: D 139 GLN cc_start: 0.7886 (tt0) cc_final: 0.7676 (pt0) REVERT: E 74 LEU cc_start: 0.7714 (mp) cc_final: 0.7365 (mt) REVERT: E 94 ARG cc_start: 0.7719 (tpt170) cc_final: 0.7284 (ttm-80) outliers start: 60 outliers final: 49 residues processed: 242 average time/residue: 0.3660 time to fit residues: 133.8514 Evaluate side-chains 232 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 181 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 448 PHE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 29 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 137 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 20550 Z= 0.292 Angle : 0.817 81.355 28099 Z= 0.338 Chirality : 0.051 1.559 3046 Planarity : 0.005 0.055 3540 Dihedral : 11.288 143.930 2923 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.18 % Allowed : 12.76 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2455 helix: 0.99 (0.15), residues: 1234 sheet: -0.47 (0.39), residues: 195 loop : -1.31 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 286 HIS 0.005 0.001 HIS B 997 PHE 0.016 0.001 PHE C 336 TYR 0.018 0.001 TYR C 269 ARG 0.005 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 183 time to evaluate : 2.140 Fit side-chains revert: symmetry clash REVERT: A 184 MET cc_start: 0.7927 (mpp) cc_final: 0.7559 (mpp) REVERT: B 212 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7348 (mm-40) REVERT: B 258 ASP cc_start: 0.6394 (t0) cc_final: 0.5822 (t0) REVERT: B 829 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 837 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7290 (t0) REVERT: C 425 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8628 (mt) REVERT: D 139 GLN cc_start: 0.7973 (tt0) cc_final: 0.7766 (pt0) REVERT: E 74 LEU cc_start: 0.7680 (mp) cc_final: 0.7338 (mt) REVERT: E 107 HIS cc_start: 0.8563 (OUTLIER) cc_final: 0.7790 (t-90) REVERT: F 401 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8339 (m110) REVERT: G 55 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6864 (mmt-90) outliers start: 65 outliers final: 54 residues processed: 234 average time/residue: 0.3637 time to fit residues: 127.6171 Evaluate side-chains 240 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 180 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 829 ILE Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 843 ILE Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 401 ASN Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain I residue 29 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 197 optimal weight: 0.0870 chunk 131 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN D 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 20550 Z= 0.174 Angle : 0.764 81.382 28099 Z= 0.312 Chirality : 0.048 1.553 3046 Planarity : 0.005 0.053 3540 Dihedral : 10.703 141.623 2923 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.15 % Allowed : 13.99 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2455 helix: 1.21 (0.15), residues: 1231 sheet: -0.44 (0.39), residues: 196 loop : -1.21 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 286 HIS 0.004 0.001 HIS C 246 PHE 0.013 0.001 PHE C 448 TYR 0.014 0.001 TYR F 104 ARG 0.002 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 2.130 Fit side-chains revert: symmetry clash REVERT: B 212 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7346 (mm-40) REVERT: B 258 ASP cc_start: 0.6378 (t0) cc_final: 0.5789 (t0) REVERT: B 616 LYS cc_start: 0.8013 (mmtm) cc_final: 0.7739 (tttt) REVERT: B 714 ARG cc_start: 0.7703 (mmt90) cc_final: 0.7356 (mmt90) REVERT: B 837 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7145 (t0) REVERT: C 425 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8554 (mt) REVERT: E 74 LEU cc_start: 0.7808 (mp) cc_final: 0.7496 (mt) REVERT: E 107 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7781 (t-90) REVERT: E 162 MET cc_start: 0.7995 (tpt) cc_final: 0.7661 (tpt) outliers start: 44 outliers final: 35 residues processed: 224 average time/residue: 0.3526 time to fit residues: 120.0568 Evaluate side-chains 222 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 448 PHE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 29 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 213 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN E 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 20550 Z= 0.224 Angle : 0.783 81.082 28099 Z= 0.321 Chirality : 0.050 1.575 3046 Planarity : 0.005 0.053 3540 Dihedral : 10.511 140.282 2921 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.59 % Allowed : 13.89 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2455 helix: 1.17 (0.15), residues: 1230 sheet: -0.36 (0.40), residues: 192 loop : -1.20 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 286 HIS 0.005 0.001 HIS C 246 PHE 0.013 0.001 PHE C 336 TYR 0.014 0.001 TYR F 104 ARG 0.003 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 187 time to evaluate : 2.171 Fit side-chains revert: symmetry clash REVERT: B 212 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7352 (mm-40) REVERT: B 258 ASP cc_start: 0.6364 (t0) cc_final: 0.5779 (t0) REVERT: B 714 ARG cc_start: 0.7716 (mmt90) cc_final: 0.7374 (mmt90) REVERT: B 837 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7263 (t0) REVERT: C 425 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8609 (mt) REVERT: E 74 LEU cc_start: 0.7816 (mp) cc_final: 0.7492 (mt) REVERT: E 107 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.7816 (t-90) REVERT: E 162 MET cc_start: 0.7912 (tpt) cc_final: 0.7658 (tpt) outliers start: 53 outliers final: 48 residues processed: 232 average time/residue: 0.3528 time to fit residues: 125.8317 Evaluate side-chains 237 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 186 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 448 PHE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 29 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 197 optimal weight: 0.0040 chunk 206 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN D 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 20550 Z= 0.168 Angle : 0.752 81.303 28099 Z= 0.306 Chirality : 0.048 1.561 3046 Planarity : 0.004 0.052 3540 Dihedral : 10.023 135.367 2921 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.10 % Allowed : 14.38 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2455 helix: 1.42 (0.15), residues: 1218 sheet: -0.40 (0.40), residues: 191 loop : -1.15 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 286 HIS 0.004 0.001 HIS C 246 PHE 0.012 0.001 PHE C 448 TYR 0.015 0.001 TYR F 104 ARG 0.002 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 189 time to evaluate : 2.245 Fit side-chains REVERT: B 82 GLN cc_start: 0.7458 (mt0) cc_final: 0.7165 (mt0) REVERT: B 212 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7377 (mm-40) REVERT: B 258 ASP cc_start: 0.6384 (t0) cc_final: 0.5802 (t0) REVERT: B 616 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7772 (tttt) REVERT: B 714 ARG cc_start: 0.7699 (mmt90) cc_final: 0.7469 (mmt90) REVERT: B 837 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7112 (t0) REVERT: C 425 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8508 (mt) REVERT: E 74 LEU cc_start: 0.7695 (mp) cc_final: 0.7423 (mt) REVERT: E 107 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.7818 (t-90) REVERT: F 133 PHE cc_start: 0.8412 (t80) cc_final: 0.8202 (t80) outliers start: 43 outliers final: 38 residues processed: 226 average time/residue: 0.3639 time to fit residues: 124.7952 Evaluate side-chains 225 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 448 PHE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 37 PHE Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 29 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 242 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 20 optimal weight: 0.0870 chunk 148 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 chunk 153 optimal weight: 2.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN E 130 GLN E 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 20550 Z= 0.299 Angle : 0.829 80.692 28099 Z= 0.342 Chirality : 0.051 1.604 3046 Planarity : 0.005 0.053 3540 Dihedral : 10.282 136.874 2921 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.25 % Allowed : 14.47 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2455 helix: 1.19 (0.15), residues: 1225 sheet: -0.43 (0.39), residues: 196 loop : -1.22 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 286 HIS 0.006 0.001 HIS B 997 PHE 0.016 0.001 PHE C 336 TYR 0.019 0.002 TYR C 269 ARG 0.004 0.000 ARG A 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 183 time to evaluate : 2.143 Fit side-chains revert: symmetry clash REVERT: B 212 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7412 (mm-40) REVERT: B 258 ASP cc_start: 0.6372 (t0) cc_final: 0.5769 (t0) REVERT: B 555 GLU cc_start: 0.6535 (mm-30) cc_final: 0.6269 (mp0) REVERT: B 714 ARG cc_start: 0.7743 (mmt90) cc_final: 0.7409 (mmt90) REVERT: C 425 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8631 (mt) REVERT: E 74 LEU cc_start: 0.7755 (mp) cc_final: 0.7436 (mt) REVERT: E 94 ARG cc_start: 0.7656 (tpt170) cc_final: 0.7330 (ttm-80) REVERT: E 107 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7732 (t-90) REVERT: E 132 ARG cc_start: 0.8080 (ttp-170) cc_final: 0.7854 (ttp-170) outliers start: 46 outliers final: 39 residues processed: 222 average time/residue: 0.3666 time to fit residues: 122.7191 Evaluate side-chains 224 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 448 PHE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain G residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 30.0000 chunk 193 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN E 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.093315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.078959 restraints weight = 32556.176| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.11 r_work: 0.2658 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 20550 Z= 0.270 Angle : 0.805 80.757 28099 Z= 0.332 Chirality : 0.051 1.598 3046 Planarity : 0.005 0.053 3540 Dihedral : 10.299 138.706 2919 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.40 % Allowed : 14.33 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2455 helix: 1.17 (0.15), residues: 1224 sheet: -0.44 (0.39), residues: 197 loop : -1.25 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 286 HIS 0.005 0.001 HIS C 246 PHE 0.015 0.001 PHE C 336 TYR 0.016 0.001 TYR C 269 ARG 0.004 0.000 ARG A 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4007.16 seconds wall clock time: 74 minutes 6.52 seconds (4446.52 seconds total)