Starting phenix.real_space_refine on Sat Feb 17 10:27:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foc_29345/02_2024/8foc_29345_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foc_29345/02_2024/8foc_29345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foc_29345/02_2024/8foc_29345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foc_29345/02_2024/8foc_29345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foc_29345/02_2024/8foc_29345_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foc_29345/02_2024/8foc_29345_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 97 5.16 5 C 11659 2.51 5 N 3156 2.21 5 O 3466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 63": "OD1" <-> "OD2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 14": "OD1" <-> "OD2" Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 503": "OD1" <-> "OD2" Residue "1 GLU 555": "OE1" <-> "OE2" Residue "1 GLU 630": "OE1" <-> "OE2" Residue "1 PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 727": "OE1" <-> "OE2" Residue "1 GLU 798": "OE1" <-> "OE2" Residue "1 PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 888": "OE1" <-> "OE2" Residue "1 TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 1035": "OD1" <-> "OD2" Residue "1 GLU 1067": "OE1" <-> "OE2" Residue "1 GLU 1111": "OE1" <-> "OE2" Residue "1 PHE 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 1209": "OD1" <-> "OD2" Residue "1 GLU 1223": "OE1" <-> "OE2" Residue "1 ASP 1273": "OD1" <-> "OD2" Residue "1 PHE 1277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 1304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 1349": "OD1" <-> "OD2" Residue "1 PHE 1396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 1424": "OE1" <-> "OE2" Residue "1 GLU 1436": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18382 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3676 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 436} Chain breaks: 4 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3257 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 375} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3412 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3388 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Conformer: "B" Number of residues, atoms: 433, 3388 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 bond proxies already assigned to first conformer: 3437 Chain: "1" Number of atoms: 8029 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1007, 7974 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1007, 7974 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8060 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3311 SG CYS B 474 39.967 98.808 76.862 1.00 12.59 S Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AASP C 263 " occ=0.82 ... (14 atoms not shown) pdb=" OD2BASP C 263 " occ=0.18 residue: pdb=" N ACYS C 399 " occ=0.46 ... (10 atoms not shown) pdb=" SG BCYS C 399 " occ=0.54 residue: pdb=" N AASN 1 745 " occ=0.33 ... (14 atoms not shown) pdb=" ND2BASN 1 745 " occ=0.67 residue: pdb=" N AGLN 1 787 " occ=0.42 ... (16 atoms not shown) pdb=" NE2BGLN 1 787 " occ=0.58 residue: pdb=" N AGLN 1 941 " occ=0.48 ... (16 atoms not shown) pdb=" NE2BGLN 1 941 " occ=0.52 residue: pdb=" N AHIS 11044 " occ=0.09 ... (18 atoms not shown) pdb=" NE2BHIS 11044 " occ=0.91 residue: pdb=" N AASP 11414 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP 11414 " occ=0.55 Time building chain proxies: 14.16, per 1000 atoms: 0.77 Number of scatterers: 18382 At special positions: 0 Unit cell: (114.264, 145.728, 154.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 97 16.00 O 3466 8.00 N 3156 7.00 C 11659 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.66 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " Number of angles added : 3 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 17 sheets defined 44.7% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 72 through 94 Processing helix chain 'B' and resid 99 through 112 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 142 through 162 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 192 through 206 removed outlier: 4.739A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.551A pdb=" N GLN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.898A pdb=" N ILE B 233 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU B 234 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 283 Proline residue: B 279 - end of helix removed outlier: 4.319A pdb=" N GLU B 283 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 298 Proline residue: B 289 - end of helix removed outlier: 3.778A pdb=" N TYR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 325 No H-bonds generated for 'chain 'B' and resid 323 through 325' Processing helix chain 'B' and resid 327 through 332 removed outlier: 4.701A pdb=" N ASN B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 347 Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 369 through 380 Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.696A pdb=" N TYR B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 435 through 438 No H-bonds generated for 'chain 'B' and resid 435 through 438' Processing helix chain 'B' and resid 441 through 450 Processing helix chain 'B' and resid 455 through 466 Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'B' and resid 500 through 526 Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 25 through 33 Processing helix chain 'A' and resid 40 through 43 No H-bonds generated for 'chain 'A' and resid 40 through 43' Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 90 through 95 removed outlier: 5.054A pdb=" N ASP A 94 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 120 removed outlier: 3.831A pdb=" N ASP A 118 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 150 removed outlier: 3.628A pdb=" N GLU A 150 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 181 through 191 Processing helix chain 'A' and resid 211 through 228 Proline residue: A 222 - end of helix removed outlier: 4.288A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 270 through 284 removed outlier: 3.715A pdb=" N ASP A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 309 removed outlier: 4.319A pdb=" N ASP A 291 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.732A pdb=" N LYS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 319' Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.516A pdb=" N LYS A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 373 through 401 Processing helix chain 'C' and resid 254 through 276 removed outlier: 3.703A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 322 through 325 No H-bonds generated for 'chain 'C' and resid 322 through 325' Processing helix chain 'C' and resid 378 through 388 Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 441 through 444 No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 461 through 468 Processing helix chain 'C' and resid 470 through 475 removed outlier: 3.709A pdb=" N THR C 475 " --> pdb=" O PRO C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 541 No H-bonds generated for 'chain 'C' and resid 538 through 541' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 556 through 567 Processing helix chain 'C' and resid 614 through 620 removed outlier: 5.072A pdb=" N GLY C 618 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 625 No H-bonds generated for 'chain 'C' and resid 623 through 625' Processing helix chain 'C' and resid 694 through 697 No H-bonds generated for 'chain 'C' and resid 694 through 697' Processing helix chain '1' and resid 403 through 418 removed outlier: 3.837A pdb=" N ILE 1 411 " --> pdb=" O HIS 1 407 " (cutoff:3.500A) Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 481 through 488 Processing helix chain '1' and resid 522 through 524 No H-bonds generated for 'chain '1' and resid 522 through 524' Processing helix chain '1' and resid 598 through 605 Processing helix chain '1' and resid 616 through 630 Processing helix chain '1' and resid 644 through 654 Processing helix chain '1' and resid 660 through 663 Processing helix chain '1' and resid 682 through 690 Processing helix chain '1' and resid 702 through 707 Processing helix chain '1' and resid 716 through 724 Processing helix chain '1' and resid 738 through 741 Processing helix chain '1' and resid 744 through 767 Processing helix chain '1' and resid 770 through 781 Processing helix chain '1' and resid 785 through 790 Processing helix chain '1' and resid 793 through 807 Processing helix chain '1' and resid 866 through 875 removed outlier: 4.261A pdb=" N TYR 1 869 " --> pdb=" O ASN 1 866 " (cutoff:3.500A) Proline residue: 1 870 - end of helix Processing helix chain '1' and resid 905 through 926 removed outlier: 3.740A pdb=" N THR 1 926 " --> pdb=" O LYS 1 922 " (cutoff:3.500A) Processing helix chain '1' and resid 930 through 955 removed outlier: 4.904A pdb=" N TYR 1 951 " --> pdb=" O ALA 1 947 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLY 1 952 " --> pdb=" O ASN 1 948 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N CYS 1 953 " --> pdb=" O SER 1 949 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU 1 954 " --> pdb=" O MET 1 950 " (cutoff:3.500A) Processing helix chain '1' and resid 964 through 987 Processing helix chain '1' and resid 1009 through 1026 Processing helix chain '1' and resid 1080 through 1093 Processing helix chain '1' and resid 1101 through 1119 Processing helix chain '1' and resid 1124 through 1127 Processing helix chain '1' and resid 1137 through 1139 No H-bonds generated for 'chain '1' and resid 1137 through 1139' Processing helix chain '1' and resid 1147 through 1158 Processing helix chain '1' and resid 1189 through 1192 No H-bonds generated for 'chain '1' and resid 1189 through 1192' Processing helix chain '1' and resid 1196 through 1200 Processing helix chain '1' and resid 1202 through 1204 No H-bonds generated for 'chain '1' and resid 1202 through 1204' Processing helix chain '1' and resid 1210 through 1215 Processing helix chain '1' and resid 1219 through 1225 removed outlier: 3.872A pdb=" N ARG 11224 " --> pdb=" O ALA 11220 " (cutoff:3.500A) Processing helix chain '1' and resid 1323 through 1342 removed outlier: 4.106A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) Processing helix chain '1' and resid 1382 through 1396 removed outlier: 3.830A pdb=" N PHE 11396 " --> pdb=" O PHE 11392 " (cutoff:3.500A) Processing helix chain '1' and resid 1398 through 1403 Processing helix chain '1' and resid 1424 through 1433 Processing helix chain '1' and resid 1435 through 1449 removed outlier: 4.157A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 225 through 228 removed outlier: 3.500A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 50 Processing sheet with id= C, first strand: chain 'A' and resid 108 through 112 Processing sheet with id= D, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.938A pdb=" N LYS C 353 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL C 362 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 340 through 342 Processing sheet with id= F, first strand: chain 'C' and resid 375 through 377 removed outlier: 4.170A pdb=" N VAL C 689 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 681 " --> pdb=" O LEU C 691 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 515 through 518 removed outlier: 6.231A pdb=" N THR C 482 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N MET C 518 " --> pdb=" O THR C 482 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU C 484 " --> pdb=" O MET C 518 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ACYS C 399 " --> pdb=" O SER C 664 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER C 664 " --> pdb=" O ACYS C 399 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 522 through 526 removed outlier: 6.680A pdb=" N ILE C 630 " --> pdb=" O GLY C 532 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER C 534 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE C 632 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL C 648 " --> pdb=" O MET C 631 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE C 633 " --> pdb=" O VAL C 648 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE C 650 " --> pdb=" O ILE C 633 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '1' and resid 525 through 527 removed outlier: 7.646A pdb=" N GLN 1 353 " --> pdb=" O LYS 1 373 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS 1 373 " --> pdb=" O GLN 1 353 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE 1 369 " --> pdb=" O LEU 1 357 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR 1 359 " --> pdb=" O ILE 1 367 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE 1 367 " --> pdb=" O TYR 1 359 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU 1 361 " --> pdb=" O THR 1 365 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR 1 365 " --> pdb=" O GLU 1 361 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL 1 515 " --> pdb=" O MET 1 383 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLN 1 385 " --> pdb=" O VAL 1 515 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL 1 517 " --> pdb=" O GLN 1 385 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '1' and resid 390 through 396 Processing sheet with id= K, first strand: chain '1' and resid 695 through 698 removed outlier: 3.617A pdb=" N SER 1 558 " --> pdb=" O GLN 1 544 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU 1 546 " --> pdb=" O ILE 1 556 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE 1 556 " --> pdb=" O LEU 1 546 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN 1 548 " --> pdb=" O GLN 1 554 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLN 1 554 " --> pdb=" O ASN 1 548 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL 1 557 " --> pdb=" O ARG 1 587 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP 1 581 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG 1 609 " --> pdb=" O THR 1 584 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL 1 586 " --> pdb=" O ARG 1 609 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG 1 611 " --> pdb=" O VAL 1 586 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '1' and resid 854 through 856 removed outlier: 6.553A pdb=" N LEU 11052 " --> pdb=" O LYS 11039 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU 11041 " --> pdb=" O ALA 11050 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA 11050 " --> pdb=" O LEU 11041 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '1' and resid 1033 through 1038 removed outlier: 3.819A pdb=" N ASP 11033 " --> pdb=" O ASP 1 864 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL 1 862 " --> pdb=" O ASP 11035 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL 11037 " --> pdb=" O VAL 1 860 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL 1 860 " --> pdb=" O VAL 11037 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP 11003 " --> pdb=" O VAL 1 992 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL 1 992 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '1' and resid 1129 through 1132 Processing sheet with id= O, first strand: chain '1' and resid 1283 through 1286 removed outlier: 4.500A pdb=" N LEU 11283 " --> pdb=" O PHE 11296 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '1' and resid 1305 through 1308 Processing sheet with id= Q, first strand: chain '1' and resid 1346 through 1348 774 hydrogen bonds defined for protein. 2113 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: 6.86 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 7746 1.42 - 1.63: 10884 1.63 - 1.85: 138 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 18780 Sorted by residual: bond pdb=" N PRO B 334 " pdb=" CD PRO B 334 " ideal model delta sigma weight residual 1.473 1.400 0.073 1.40e-02 5.10e+03 2.75e+01 bond pdb=" N PRO B 334 " pdb=" CA PRO B 334 " ideal model delta sigma weight residual 1.464 1.419 0.044 9.30e-03 1.16e+04 2.24e+01 bond pdb=" CG PRO A 374 " pdb=" CD PRO A 374 " ideal model delta sigma weight residual 1.503 1.345 0.158 3.40e-02 8.65e+02 2.17e+01 bond pdb=" N PRO 1 574 " pdb=" CA PRO 1 574 " ideal model delta sigma weight residual 1.464 1.422 0.041 9.30e-03 1.16e+04 1.95e+01 bond pdb=" CE1 HIS 1 803 " pdb=" NE2 HIS 1 803 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.64e+01 ... (remaining 18775 not shown) Histogram of bond angle deviations from ideal: 73.56 - 85.86: 12 85.86 - 98.16: 6 98.16 - 110.45: 4683 110.45 - 122.75: 19099 122.75 - 135.05: 1638 Bond angle restraints: 25438 Sorted by residual: angle pdb=" N PRO A 374 " pdb=" CD PRO A 374 " pdb=" CG PRO A 374 " ideal model delta sigma weight residual 103.20 93.68 9.52 1.50e+00 4.44e-01 4.03e+01 angle pdb=" CA PRO A 374 " pdb=" CB PRO A 374 " pdb=" CG PRO A 374 " ideal model delta sigma weight residual 104.50 93.08 11.42 1.90e+00 2.77e-01 3.61e+01 angle pdb=" CA PRO 1 534 " pdb=" N PRO 1 534 " pdb=" CD PRO 1 534 " ideal model delta sigma weight residual 112.00 104.33 7.67 1.40e+00 5.10e-01 3.00e+01 angle pdb=" CA PRO A 374 " pdb=" N PRO A 374 " pdb=" CD PRO A 374 " ideal model delta sigma weight residual 112.00 104.79 7.21 1.40e+00 5.10e-01 2.65e+01 angle pdb=" C ASN B 332 " pdb=" N TYR B 333 " pdb=" CA TYR B 333 " ideal model delta sigma weight residual 121.92 113.89 8.03 1.60e+00 3.91e-01 2.52e+01 ... (remaining 25433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10354 17.95 - 35.90: 871 35.90 - 53.85: 192 53.85 - 71.80: 40 71.80 - 89.75: 19 Dihedral angle restraints: 11476 sinusoidal: 4687 harmonic: 6789 Sorted by residual: dihedral pdb=" CA GLU 1 409 " pdb=" C GLU 1 409 " pdb=" N ILE 1 410 " pdb=" CA ILE 1 410 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA VAL 11362 " pdb=" C VAL 11362 " pdb=" N PHE 11363 " pdb=" CA PHE 11363 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA LEU 1 640 " pdb=" C LEU 1 640 " pdb=" N GLN 1 641 " pdb=" CA GLN 1 641 " ideal model delta harmonic sigma weight residual -180.00 -161.20 -18.80 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 11473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2187 0.048 - 0.097: 485 0.097 - 0.145: 130 0.145 - 0.194: 9 0.194 - 0.242: 4 Chirality restraints: 2815 Sorted by residual: chirality pdb=" CB ILE 1 507 " pdb=" CA ILE 1 507 " pdb=" CG1 ILE 1 507 " pdb=" CG2 ILE 1 507 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE 1 367 " pdb=" CA ILE 1 367 " pdb=" CG1 ILE 1 367 " pdb=" CG2 ILE 1 367 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE 11207 " pdb=" N ILE 11207 " pdb=" C ILE 11207 " pdb=" CB ILE 11207 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2812 not shown) Planarity restraints: 3315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 470 " 0.071 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO C 471 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO C 471 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 471 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 1 450 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.75e+00 pdb=" N PRO 1 451 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO 1 451 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO 1 451 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 65 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO B 66 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 66 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 66 " 0.039 5.00e-02 4.00e+02 ... (remaining 3312 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3298 2.77 - 3.30: 18032 3.30 - 3.83: 30707 3.83 - 4.37: 36532 4.37 - 4.90: 62077 Nonbonded interactions: 150646 Sorted by model distance: nonbonded pdb=" OD1 ASP B 416 " pdb=" OG1 THR B 419 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR A 122 " pdb=" O GLN A 232 " model vdw 2.236 2.440 nonbonded pdb=" O ALA C 444 " pdb=" NE2 GLN 11329 " model vdw 2.256 2.520 nonbonded pdb=" OD2 ASP A 151 " pdb=" OH TYR A 190 " model vdw 2.265 2.440 nonbonded pdb=" O THR 1 708 " pdb=" OG1 THR 1 708 " model vdw 2.265 2.440 ... (remaining 150641 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 4.320 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 58.810 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 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 : 0.005 0.158 18780 Z= 0.310 Angle : 0.672 12.648 25438 Z= 0.392 Chirality : 0.044 0.242 2815 Planarity : 0.005 0.103 3315 Dihedral : 14.503 89.747 7068 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.46 % Favored : 98.45 % Rotamer: Outliers : 0.39 % Allowed : 11.56 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 1.23 (0.17), residues: 2285 helix: 1.53 (0.16), residues: 1067 sheet: 0.11 (0.29), residues: 261 loop : 0.35 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 356 HIS 0.007 0.001 HIS B 401 PHE 0.034 0.002 PHE C 310 TYR 0.021 0.002 TYR B 333 ARG 0.004 0.000 ARG C 513 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 333 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 410 ILE cc_start: 0.7821 (mt) cc_final: 0.7461 (mt) REVERT: C 262 ASP cc_start: 0.6287 (t0) cc_final: 0.5936 (t0) REVERT: C 332 LEU cc_start: 0.6445 (mt) cc_final: 0.5382 (tp) REVERT: C 356 ASN cc_start: 0.7335 (p0) cc_final: 0.6958 (p0) REVERT: C 514 ASN cc_start: 0.7061 (p0) cc_final: 0.6760 (p0) REVERT: 1 491 ILE cc_start: 0.7658 (mm) cc_final: 0.7328 (mt) REVERT: 1 703 MET cc_start: 0.7965 (tpp) cc_final: 0.7567 (tpp) REVERT: 1 713 SER cc_start: 0.7956 (p) cc_final: 0.7422 (t) REVERT: 1 783 ASN cc_start: 0.8032 (p0) cc_final: 0.7787 (p0) REVERT: 1 1302 SER cc_start: 0.8176 (t) cc_final: 0.7782 (m) outliers start: 8 outliers final: 1 residues processed: 338 average time/residue: 0.3052 time to fit residues: 156.9674 Evaluate side-chains 231 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 1322 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 HIS ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN A 253 GLN A 373 GLN C 693 ASN 1 473 HIS 1 683 ASN 1 736 GLN 1 776 GLN 1 779 ASN ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 874 GLN 1 931 HIS 1 972 ASN ** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN ** 11329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18780 Z= 0.326 Angle : 0.660 10.480 25438 Z= 0.338 Chirality : 0.046 0.193 2815 Planarity : 0.006 0.085 3315 Dihedral : 4.665 59.681 2502 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.66 % Allowed : 12.55 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.76 (0.17), residues: 2285 helix: 1.09 (0.15), residues: 1063 sheet: -0.17 (0.29), residues: 266 loop : 0.21 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 78 HIS 0.011 0.002 HIS 11337 PHE 0.032 0.003 PHE C 268 TYR 0.026 0.002 TYR 1 735 ARG 0.006 0.001 ARG 11276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 245 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 410 ILE cc_start: 0.7904 (mt) cc_final: 0.7533 (mt) REVERT: C 262 ASP cc_start: 0.6523 (t0) cc_final: 0.6189 (t0) REVERT: 1 469 ASP cc_start: 0.6441 (OUTLIER) cc_final: 0.6227 (m-30) REVERT: 1 482 PHE cc_start: 0.8747 (t80) cc_final: 0.8446 (t80) REVERT: 1 491 ILE cc_start: 0.7999 (mm) cc_final: 0.7684 (mt) REVERT: 1 906 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7353 (tt) REVERT: 1 1302 SER cc_start: 0.8742 (t) cc_final: 0.8324 (m) outliers start: 54 outliers final: 41 residues processed: 283 average time/residue: 0.2840 time to fit residues: 126.2955 Evaluate side-chains 255 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 212 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 364 ASN Chi-restraints excluded: chain 1 residue 469 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 505 ASN Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 545 THR Chi-restraints excluded: chain 1 residue 559 ILE Chi-restraints excluded: chain 1 residue 627 LEU Chi-restraints excluded: chain 1 residue 663 ILE Chi-restraints excluded: chain 1 residue 667 LEU Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 879 CYS Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 906 LEU Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1322 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 HIS B 432 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 HIS A 253 GLN 1 428 GLN ** 1 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN 11044 HIS B 11211 GLN 11388 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 18780 Z= 0.379 Angle : 0.668 10.203 25438 Z= 0.344 Chirality : 0.047 0.177 2815 Planarity : 0.006 0.075 3315 Dihedral : 4.811 55.244 2502 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.59 % Allowed : 13.68 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.13 (0.17), residues: 2285 helix: 0.72 (0.16), residues: 1057 sheet: -0.71 (0.29), residues: 274 loop : -0.22 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 695 HIS 0.012 0.002 HIS 11337 PHE 0.029 0.002 PHE C 268 TYR 0.027 0.002 TYR B 333 ARG 0.006 0.001 ARG 11021 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 224 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.7064 (m-10) REVERT: B 119 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: B 121 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7232 (mt) REVERT: B 128 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6573 (m-80) REVERT: B 401 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7882 (t70) REVERT: B 410 ILE cc_start: 0.7917 (mt) cc_final: 0.7520 (mt) REVERT: A 100 GLU cc_start: 0.4822 (mm-30) cc_final: 0.4576 (mm-30) REVERT: C 262 ASP cc_start: 0.6412 (t0) cc_final: 0.6111 (t0) REVERT: C 504 ILE cc_start: 0.8619 (mt) cc_final: 0.8310 (pt) REVERT: 1 469 ASP cc_start: 0.6506 (OUTLIER) cc_final: 0.6283 (m-30) REVERT: 1 491 ILE cc_start: 0.8075 (mm) cc_final: 0.7815 (mt) outliers start: 73 outliers final: 48 residues processed: 280 average time/residue: 0.2799 time to fit residues: 122.4323 Evaluate side-chains 255 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 201 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 364 ASN Chi-restraints excluded: chain 1 residue 469 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 505 ASN Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 545 THR Chi-restraints excluded: chain 1 residue 627 LEU Chi-restraints excluded: chain 1 residue 663 ILE Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 875 GLU Chi-restraints excluded: chain 1 residue 879 CYS Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 988 MET Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1067 GLU Chi-restraints excluded: chain 1 residue 1113 ILE Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1322 THR Chi-restraints excluded: chain 1 residue 1440 THR Chi-restraints excluded: chain 1 residue 1443 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 219 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 373 GLN ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18780 Z= 0.181 Angle : 0.517 8.997 25438 Z= 0.265 Chirality : 0.041 0.165 2815 Planarity : 0.005 0.070 3315 Dihedral : 4.377 58.792 2502 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.36 % Allowed : 14.86 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.62 (0.17), residues: 2285 helix: 1.09 (0.16), residues: 1049 sheet: -0.59 (0.30), residues: 275 loop : 0.12 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.005 0.001 HIS A 212 PHE 0.018 0.001 PHE 1 485 TYR 0.021 0.001 TYR B 333 ARG 0.004 0.000 ARG C 513 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 220 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.6525 (m-80) REVERT: B 219 PHE cc_start: 0.7283 (t80) cc_final: 0.7050 (t80) REVERT: B 298 TYR cc_start: 0.5660 (t80) cc_final: 0.4916 (t80) REVERT: B 410 ILE cc_start: 0.7885 (mt) cc_final: 0.7501 (mt) REVERT: C 262 ASP cc_start: 0.6374 (t0) cc_final: 0.6050 (t0) REVERT: C 504 ILE cc_start: 0.8533 (mt) cc_final: 0.8262 (pt) REVERT: 1 491 ILE cc_start: 0.7944 (mm) cc_final: 0.7706 (mt) REVERT: 1 1027 TYR cc_start: 0.5959 (m-80) cc_final: 0.5637 (m-80) REVERT: 1 1302 SER cc_start: 0.8782 (t) cc_final: 0.8441 (m) outliers start: 48 outliers final: 33 residues processed: 257 average time/residue: 0.2865 time to fit residues: 117.1923 Evaluate side-chains 225 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 505 ASN Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 557 VAL Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 875 GLU Chi-restraints excluded: chain 1 residue 879 CYS Chi-restraints excluded: chain 1 residue 988 MET Chi-restraints excluded: chain 1 residue 1067 GLU Chi-restraints excluded: chain 1 residue 1449 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 6.9990 chunk 124 optimal weight: 0.0060 chunk 3 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 90 optimal weight: 0.1980 chunk 187 optimal weight: 2.9990 chunk 151 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 HIS C 567 GLN 1 544 GLN 1 576 ASN 1 754 ASN ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18780 Z= 0.141 Angle : 0.494 9.664 25438 Z= 0.251 Chirality : 0.041 0.220 2815 Planarity : 0.004 0.065 3315 Dihedral : 3.952 19.084 2501 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.31 % Allowed : 15.75 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.94 (0.17), residues: 2285 helix: 1.39 (0.16), residues: 1055 sheet: -0.56 (0.30), residues: 276 loop : 0.29 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.004 0.001 HIS B 131 PHE 0.019 0.001 PHE 1 485 TYR 0.029 0.001 TYR C 295 ARG 0.002 0.000 ARG C 662 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 209 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6857 (m-10) REVERT: B 219 PHE cc_start: 0.7209 (t80) cc_final: 0.6987 (t80) REVERT: B 410 ILE cc_start: 0.7905 (mt) cc_final: 0.7505 (mt) REVERT: A 361 MET cc_start: 0.6456 (mmm) cc_final: 0.6124 (mmm) REVERT: C 262 ASP cc_start: 0.6211 (t0) cc_final: 0.5892 (t0) REVERT: 1 924 MET cc_start: 0.6788 (ttm) cc_final: 0.6579 (ttm) REVERT: 1 1027 TYR cc_start: 0.5980 (m-80) cc_final: 0.5745 (m-80) REVERT: 1 1302 SER cc_start: 0.8753 (t) cc_final: 0.8427 (m) outliers start: 47 outliers final: 35 residues processed: 244 average time/residue: 0.2698 time to fit residues: 106.5665 Evaluate side-chains 228 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 505 ASN Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 544 GLN Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 988 MET Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1067 GLU Chi-restraints excluded: chain 1 residue 1136 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 8.9990 chunk 197 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN 1 754 ASN 1 783 ASN 1 989 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18780 Z= 0.178 Angle : 0.507 10.198 25438 Z= 0.256 Chirality : 0.041 0.162 2815 Planarity : 0.004 0.063 3315 Dihedral : 3.925 18.453 2501 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.85 % Allowed : 15.80 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2285 helix: 1.41 (0.16), residues: 1057 sheet: -0.54 (0.29), residues: 271 loop : 0.27 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 325 HIS 0.004 0.001 HIS 11337 PHE 0.020 0.001 PHE C 655 TYR 0.023 0.001 TYR C 295 ARG 0.003 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 192 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6972 (m-10) REVERT: B 128 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6530 (m-80) REVERT: B 219 PHE cc_start: 0.7224 (t80) cc_final: 0.6973 (t80) REVERT: B 410 ILE cc_start: 0.7971 (mt) cc_final: 0.7569 (mt) REVERT: 1 924 MET cc_start: 0.6827 (ttm) cc_final: 0.6611 (ttm) REVERT: 1 1027 TYR cc_start: 0.5999 (m-80) cc_final: 0.5792 (m-80) outliers start: 58 outliers final: 47 residues processed: 237 average time/residue: 0.2826 time to fit residues: 107.5017 Evaluate side-chains 235 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 186 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 505 ASN Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 545 THR Chi-restraints excluded: chain 1 residue 557 VAL Chi-restraints excluded: chain 1 residue 783 ASN Chi-restraints excluded: chain 1 residue 814 ASP Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 875 GLU Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 988 MET Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1067 GLU Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1322 THR Chi-restraints excluded: chain 1 residue 1377 ARG Chi-restraints excluded: chain 1 residue 1449 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 160 optimal weight: 0.4980 chunk 124 optimal weight: 0.5980 chunk 184 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 218 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 373 GLN ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN 11044 HIS A Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18780 Z= 0.184 Angle : 0.509 9.175 25438 Z= 0.258 Chirality : 0.041 0.154 2815 Planarity : 0.004 0.063 3315 Dihedral : 3.903 18.173 2501 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.81 % Allowed : 16.14 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.95 (0.18), residues: 2285 helix: 1.46 (0.16), residues: 1048 sheet: -0.59 (0.29), residues: 271 loop : 0.21 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 1 785 HIS 0.005 0.001 HIS C 427 PHE 0.016 0.001 PHE 1 485 TYR 0.022 0.001 TYR B 333 ARG 0.003 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 198 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6945 (m-10) REVERT: B 127 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7172 (t0) REVERT: B 128 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6532 (m-80) REVERT: B 219 PHE cc_start: 0.7220 (t80) cc_final: 0.6967 (t80) REVERT: B 410 ILE cc_start: 0.7993 (mt) cc_final: 0.7574 (mt) REVERT: A 190 TYR cc_start: 0.6539 (t80) cc_final: 0.6274 (t80) REVERT: 1 866 ASN cc_start: 0.6548 (m-40) cc_final: 0.6274 (m110) REVERT: 1 924 MET cc_start: 0.6785 (ttm) cc_final: 0.6561 (ttm) outliers start: 57 outliers final: 47 residues processed: 244 average time/residue: 0.2674 time to fit residues: 105.0751 Evaluate side-chains 235 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 185 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 505 ASN Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 557 VAL Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 814 ASP Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 875 GLU Chi-restraints excluded: chain 1 residue 879 CYS Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 988 MET Chi-restraints excluded: chain 1 residue 1034 ILE Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1067 GLU Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1322 THR Chi-restraints excluded: chain 1 residue 1377 ARG Chi-restraints excluded: chain 1 residue 1449 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 42 optimal weight: 0.2980 chunk 139 optimal weight: 5.9990 chunk 149 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN 1 554 GLN 1 989 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18780 Z= 0.137 Angle : 0.488 9.475 25438 Z= 0.247 Chirality : 0.040 0.175 2815 Planarity : 0.004 0.059 3315 Dihedral : 3.753 18.011 2501 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.31 % Allowed : 16.73 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 1.11 (0.18), residues: 2285 helix: 1.59 (0.16), residues: 1045 sheet: -0.56 (0.30), residues: 271 loop : 0.33 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.003 0.001 HIS B 131 PHE 0.034 0.001 PHE 1 485 TYR 0.021 0.001 TYR B 333 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 203 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6887 (m-10) REVERT: B 128 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6514 (m-80) REVERT: B 219 PHE cc_start: 0.7195 (t80) cc_final: 0.6932 (t80) REVERT: B 410 ILE cc_start: 0.7970 (mt) cc_final: 0.7568 (mt) REVERT: 1 1302 SER cc_start: 0.8697 (t) cc_final: 0.8335 (m) outliers start: 47 outliers final: 36 residues processed: 241 average time/residue: 0.2707 time to fit residues: 104.3781 Evaluate side-chains 228 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 505 ASN Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 545 THR Chi-restraints excluded: chain 1 residue 557 VAL Chi-restraints excluded: chain 1 residue 663 ILE Chi-restraints excluded: chain 1 residue 814 ASP Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 988 MET Chi-restraints excluded: chain 1 residue 1034 ILE Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1322 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 0.0870 chunk 191 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 160 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 GLN 1 783 ASN 1 989 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18780 Z= 0.147 Angle : 0.506 14.863 25438 Z= 0.254 Chirality : 0.040 0.200 2815 Planarity : 0.004 0.059 3315 Dihedral : 3.704 17.617 2501 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.21 % Allowed : 16.83 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 1.17 (0.18), residues: 2285 helix: 1.66 (0.16), residues: 1039 sheet: -0.57 (0.29), residues: 277 loop : 0.36 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 325 HIS 0.003 0.001 HIS B 131 PHE 0.031 0.001 PHE 1 485 TYR 0.020 0.001 TYR B 333 ARG 0.004 0.000 ARG 1 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 194 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6984 (m-10) REVERT: B 128 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6523 (m-80) REVERT: B 219 PHE cc_start: 0.7172 (t80) cc_final: 0.6913 (t80) REVERT: B 410 ILE cc_start: 0.7985 (mt) cc_final: 0.7582 (mt) REVERT: 1 1302 SER cc_start: 0.8695 (t) cc_final: 0.8332 (m) outliers start: 45 outliers final: 42 residues processed: 230 average time/residue: 0.2646 time to fit residues: 98.7757 Evaluate side-chains 236 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 192 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 505 ASN Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 545 THR Chi-restraints excluded: chain 1 residue 557 VAL Chi-restraints excluded: chain 1 residue 663 ILE Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 783 ASN Chi-restraints excluded: chain 1 residue 814 ASP Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 988 MET Chi-restraints excluded: chain 1 residue 1034 ILE Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1322 THR Chi-restraints excluded: chain 1 residue 1377 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 149 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.169 18780 Z= 0.191 Angle : 0.706 59.001 25438 Z= 0.399 Chirality : 0.044 0.871 2815 Planarity : 0.004 0.059 3315 Dihedral : 3.749 29.027 2501 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.73 % Favored : 98.23 % Rotamer: Outliers : 2.12 % Allowed : 16.78 % Favored : 81.10 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.31 % 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: 1.16 (0.18), residues: 2285 helix: 1.65 (0.16), residues: 1039 sheet: -0.57 (0.29), residues: 277 loop : 0.36 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 325 HIS 0.003 0.001 HIS B 131 PHE 0.029 0.001 PHE 1 485 TYR 0.020 0.001 TYR B 333 ARG 0.004 0.000 ARG 1 490 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 192 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6990 (m-10) REVERT: B 128 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6528 (m-80) REVERT: B 219 PHE cc_start: 0.7182 (t80) cc_final: 0.6923 (t80) REVERT: B 410 ILE cc_start: 0.7985 (mt) cc_final: 0.7582 (mt) REVERT: 1 1302 SER cc_start: 0.8696 (t) cc_final: 0.8339 (m) outliers start: 43 outliers final: 40 residues processed: 226 average time/residue: 0.2641 time to fit residues: 97.0328 Evaluate side-chains 232 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 190 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 505 ASN Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 557 VAL Chi-restraints excluded: chain 1 residue 663 ILE Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 814 ASP Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 988 MET Chi-restraints excluded: chain 1 residue 1034 ILE Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1322 THR Chi-restraints excluded: chain 1 residue 1377 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.152149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139732 restraints weight = 111292.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.141592 restraints weight = 108592.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141826 restraints weight = 62050.374| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.169 18780 Z= 0.191 Angle : 0.706 59.000 25438 Z= 0.399 Chirality : 0.044 0.870 2815 Planarity : 0.004 0.059 3315 Dihedral : 3.749 29.023 2501 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.73 % Favored : 98.23 % Rotamer: Outliers : 2.07 % Allowed : 16.78 % Favored : 81.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.31 % 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: 1.16 (0.18), residues: 2285 helix: 1.65 (0.16), residues: 1039 sheet: -0.57 (0.29), residues: 277 loop : 0.36 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 325 HIS 0.003 0.001 HIS B 131 PHE 0.029 0.001 PHE 1 485 TYR 0.020 0.001 TYR B 333 ARG 0.004 0.000 ARG 1 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3384.47 seconds wall clock time: 63 minutes 7.54 seconds (3787.54 seconds total)