Starting phenix.real_space_refine on Thu Apr 11 19:37:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/04_2024/6zp5_11336_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/04_2024/6zp5_11336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/04_2024/6zp5_11336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/04_2024/6zp5_11336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/04_2024/6zp5_11336_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/04_2024/6zp5_11336_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 14927 2.51 5 N 3780 2.21 5 O 4807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 26": "OD1" <-> "OD2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ASP 541": "OD1" <-> "OD2" Residue "A ASP 547": "OD1" <-> "OD2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 559": "OD1" <-> "OD2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ASP 636": "OD1" <-> "OD2" Residue "A ASP 710": "OD1" <-> "OD2" Residue "A ASP 718": "OD1" <-> "OD2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A ARG 788": "NH1" <-> "NH2" Residue "A GLU 841": "OE1" <-> "OE2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A ASP 967": "OD1" <-> "OD2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ASP 1091": "OD1" <-> "OD2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B ASP 260": "OD1" <-> "OD2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "B ASP 324": "OD1" <-> "OD2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B ASP 496": "OD1" <-> "OD2" Residue "B TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 566": "OD1" <-> "OD2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 782": "OD1" <-> "OD2" Residue "B GLU 785": "OE1" <-> "OE2" Residue "B GLU 889": "OE1" <-> "OE2" Residue "B ASP 924": "OD1" <-> "OD2" Residue "B GLU 941": "OE1" <-> "OE2" Residue "C PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 14": "OD1" <-> "OD2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 490": "OE1" <-> "OE2" Residue "C ASP 542": "OD1" <-> "OD2" Residue "C ASP 588": "OD1" <-> "OD2" Residue "C GLU 635": "OE1" <-> "OE2" Residue "C TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 782": "OD1" <-> "OD2" Residue "C ARG 789": "NH1" <-> "NH2" Residue "C PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 953": "OD1" <-> "OD2" Residue "C GLU 964": "OE1" <-> "OE2" Residue "C GLU 991": "OE1" <-> "OE2" Residue "C GLU 1066": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23615 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7709 Classifications: {'peptide': 988} Link IDs: {'PTRANS': 48, 'TRANS': 939} Chain breaks: 8 Chain: "B" Number of atoms: 7367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7367 Classifications: {'peptide': 943} Link IDs: {'PTRANS': 45, 'TRANS': 897} Chain breaks: 12 Chain: "C" Number of atoms: 7243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7243 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 44, 'TRANS': 885} Chain breaks: 10 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 114 Unusual residues: {'DMS': 3, 'MAN': 1, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 12.49, per 1000 atoms: 0.53 Number of scatterers: 23615 At special positions: 0 Unit cell: (127.734, 130.875, 195.789, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 4807 8.00 N 3780 7.00 C 14927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 274 " distance=2.00 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 334 " distance=2.05 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 405 " distance=2.06 Simple disulfide: pdb=" SG CYS A 453 " - pdb=" SG CYS A 461 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 563 " distance=2.04 Simple disulfide: pdb=" SG CYS A 590 " - pdb=" SG CYS A 622 " distance=1.97 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 733 " distance=2.02 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 722 " distance=2.05 Simple disulfide: pdb=" SG CYS A1005 " - pdb=" SG CYS A1016 " distance=2.01 Simple disulfide: pdb=" SG CYS A1055 " - pdb=" SG CYS A1099 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 98 " distance=1.77 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 197 " distance=2.05 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 376 " distance=2.01 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 441 " distance=2.08 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 482 " distance=2.01 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 504 " distance=2.02 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 581 " distance=2.02 Simple disulfide: pdb=" SG CYS B 564 " - pdb=" SG CYS B 570 " distance=2.05 Simple disulfide: pdb=" SG CYS B 829 " - pdb=" SG CYS B 840 " distance=2.02 Simple disulfide: pdb=" SG CYS B 879 " - pdb=" SG CYS B 923 " distance=2.03 Simple disulfide: pdb=" SG CYS C 265 " - pdb=" SG CYS C 275 " distance=2.07 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 353 " - pdb=" SG CYS C 406 " distance=2.02 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 499 " distance=2.03 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS C 564 " distance=2.00 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 623 " distance=2.02 Simple disulfide: pdb=" SG CYS C 636 " - pdb=" SG CYS C 645 " distance=2.01 Simple disulfide: pdb=" SG CYS C 712 " - pdb=" SG CYS C 734 " distance=2.03 Simple disulfide: pdb=" SG CYS C 717 " - pdb=" SG CYS C 723 " distance=2.04 Simple disulfide: pdb=" SG CYS C1006 " - pdb=" SG CYS C1017 " distance=2.05 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1100 " distance=2.03 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 Atom "HETATM23556 O5 NAG C1301 .*. O " rejected from bonding due to valence issues. Atom "HETATM23586 O5 NAG C1303 .*. O " rejected from bonding due to valence issues. Atom "HETATM22680 O5 NAG N 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 316 " " NAG A1302 " - " ASN A 576 " " NAG A1303 " - " ASN A 589 " " NAG A1304 " - " ASN A 95 " " NAG A1305 " - " ASN A 138 " " NAG A1306 " - " ASN A 207 " " NAG B1101 " - " ASN B 227 " " NAG B1102 " - " ASN B 467 " " NAG B1103 " - " ASN B 490 " " NAG B1104 " - " ASN B 239 " " NAG B1105 " - " ASN B 97 " " NAG B1106 " - " ASN B 35 " " NAG B1107 " - " ASN B 454 " " NAG B1108 " - " ASN B 81 " " NAG C1301 " - " ASN C 590 " " NAG C1302 " - " ASN C 577 " " NAG C1303 " - " ASN C 305 " " NAG C1305 " - " ASN C 139 " " NAG D 1 " - " ASN A 630 " " NAG E 1 " - " ASN A 690 " " NAG F 1 " - " ASN A 774 " " NAG G 1 " - " ASN A1047 " " NAG H 1 " - " ASN A1071 " " NAG I 1 " - " ASN A1107 " " NAG J 1 " - " ASN A 255 " " NAG K 1 " - " ASN A 304 " " NAG L 1 " - " ASN A 682 " " NAG M 1 " - " ASN B 530 " " NAG N 1 " - " ASN B 931 " " NAG O 1 " - " ASN B 871 " " NAG P 1 " - " ASN B 895 " " NAG Q 1 " - " ASN B 622 " " NAG R 1 " - " ASN B 538 " " NAG S 1 " - " ASN B 178 " " NAG T 1 " - " ASN B 151 " " NAG U 1 " - " ASN C1108 " " NAG V 1 " - " ASN C1072 " " NAG W 1 " - " ASN C1048 " " NAG X 1 " - " ASN C 775 " " NAG Y 1 " - " ASN C 691 " " NAG Z 1 " - " ASN C 683 " " NAG a 1 " - " ASN C 256 " " NAG b 1 " - " ASN C 317 " " NAG c 1 " - " ASN C 96 " " NAG d 1 " - " ASN C 631 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.21 Conformation dependent library (CDL) restraints added in 3.7 seconds 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 42 sheets defined 23.7% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.04 Creating SS restraints... Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 312 through 315 No H-bonds generated for 'chain 'A' and resid 312 through 315' Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 377 through 382 removed outlier: 4.383A pdb=" N ARG A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 382' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 720 through 729 removed outlier: 3.677A pdb=" N LEU A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 755 removed outlier: 3.719A pdb=" N ASP A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 840 through 856 Processing helix chain 'A' and resid 860 through 863 No H-bonds generated for 'chain 'A' and resid 860 through 863' Processing helix chain 'A' and resid 871 through 882 removed outlier: 3.751A pdb=" N ILE A 882 " --> pdb=" O ARG A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 893 through 912 Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.130A pdb=" N LEU A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER A 940 " --> pdb=" O VAL A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 955 Processing helix chain 'A' and resid 959 through 1004 removed outlier: 4.136A pdb=" N VAL A 964 " --> pdb=" O PRO A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1119 removed outlier: 4.152A pdb=" N GLU A1117 " --> pdb=" O PRO A1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 313 through 316 No H-bonds generated for 'chain 'B' and resid 313 through 316' Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.929A pdb=" N GLN B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 603 removed outlier: 3.503A pdb=" N ASP B 596 " --> pdb=" O ALA B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 684 through 687 No H-bonds generated for 'chain 'B' and resid 684 through 687' Processing helix chain 'B' and resid 695 through 706 Processing helix chain 'B' and resid 710 through 715 removed outlier: 3.880A pdb=" N GLU B 715 " --> pdb=" O VAL B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 737 Processing helix chain 'B' and resid 743 through 764 removed outlier: 4.206A pdb=" N LEU B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER B 764 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 779 Processing helix chain 'B' and resid 783 through 829 removed outlier: 3.951A pdb=" N VAL B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 793 " --> pdb=" O GLN B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 942 removed outlier: 3.700A pdb=" N GLU B 941 " --> pdb=" O PRO B 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 277 Processing helix chain 'C' and resid 313 through 316 No H-bonds generated for 'chain 'C' and resid 313 through 316' Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 358 through 362 removed outlier: 4.125A pdb=" N ASN C 362 " --> pdb=" O THR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 383 removed outlier: 4.370A pdb=" N ARG C 382 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 395 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 712 through 717 Processing helix chain 'C' and resid 721 through 728 Processing helix chain 'C' and resid 733 through 756 removed outlier: 3.548A pdb=" N ASP C 749 " --> pdb=" O ALA C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 799 Processing helix chain 'C' and resid 841 through 858 Processing helix chain 'C' and resid 861 through 864 No H-bonds generated for 'chain 'C' and resid 861 through 864' Processing helix chain 'C' and resid 872 through 883 Processing helix chain 'C' and resid 887 through 892 removed outlier: 3.936A pdb=" N GLU C 892 " --> pdb=" O VAL C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 914 removed outlier: 3.600A pdb=" N GLN C 909 " --> pdb=" O ILE C 905 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 910 " --> pdb=" O GLY C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 941 removed outlier: 4.123A pdb=" N LEU C 940 " --> pdb=" O LEU C 936 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER C 941 " --> pdb=" O VAL C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 956 Processing helix chain 'C' and resid 960 through 1006 removed outlier: 4.238A pdb=" N VAL C 965 " --> pdb=" O PRO C 961 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1120 removed outlier: 4.175A pdb=" N GLU C1118 " --> pdb=" O PRO C1114 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 removed outlier: 3.763A pdb=" N SER A 33 " --> pdb=" O SER A 4 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 21 through 24 removed outlier: 3.765A pdb=" N ASP A 260 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 36 through 38 removed outlier: 3.537A pdb=" N ILE A 176 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 200 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER A 178 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 77 through 79 Processing sheet with id= E, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= F, first strand: chain 'A' and resid 299 through 301 Processing sheet with id= G, first strand: chain 'A' and resid 327 through 331 removed outlier: 4.064A pdb=" N VAL A 368 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 425 through 427 Processing sheet with id= I, first strand: chain 'A' and resid 524 through 527 removed outlier: 3.878A pdb=" N GLU A 556 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP A 547 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY A 539 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 615 through 618 removed outlier: 4.941A pdb=" N GLY A 567 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 570 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLN A 287 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR A 572 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE A 285 " --> pdb=" O THR A 572 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 644 through 648 Processing sheet with id= L, first strand: chain 'A' and resid 684 through 688 removed outlier: 3.746A pdb=" N ALA A1051 " --> pdb=" O PHE A1068 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE A1068 " --> pdb=" O ALA A1051 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 690 through 701 removed outlier: 6.029A pdb=" N TYR A1040 " --> pdb=" O HIS A1021 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS A1021 " --> pdb=" O TYR A1040 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 706 through 709 removed outlier: 4.434A pdb=" N LYS A 706 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1053 through 1056 Processing sheet with id= P, first strand: chain 'B' and resid 2 through 4 removed outlier: 6.962A pdb=" N ASN B 35 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR B 165 " --> pdb=" O ASN B 35 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.763A pdb=" N ASP B 183 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 62 through 65 Processing sheet with id= S, first strand: chain 'B' and resid 86 through 88 Processing sheet with id= T, first strand: chain 'B' and resid 222 through 224 removed outlier: 5.250A pdb=" N ASP B 425 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY B 417 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 250 through 254 Processing sheet with id= V, first strand: chain 'B' and resid 475 through 477 removed outlier: 4.267A pdb=" N GLY B 445 " --> pdb=" O GLN B 464 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 212 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 448 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLN B 210 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR B 450 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE B 208 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 513 through 517 removed outlier: 6.470A pdb=" N ALA B 505 " --> pdb=" O PRO B 498 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 532 through 536 Processing sheet with id= Y, first strand: chain 'B' and resid 538 through 549 removed outlier: 6.177A pdb=" N TYR B 864 " --> pdb=" O HIS B 845 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N HIS B 845 " --> pdb=" O TYR B 864 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 555 through 557 Processing sheet with id= AA, first strand: chain 'B' and resid 877 through 879 Processing sheet with id= AB, first strand: chain 'B' and resid 891 through 894 Processing sheet with id= AC, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= AD, first strand: chain 'C' and resid 22 through 25 removed outlier: 3.679A pdb=" N ASP C 261 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 28 through 30 Processing sheet with id= AF, first strand: chain 'C' and resid 238 through 243 removed outlier: 4.253A pdb=" N ALA C 238 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 69 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER C 68 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 164 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 100 through 103 Processing sheet with id= AH, first strand: chain 'C' and resid 300 through 302 removed outlier: 3.823A pdb=" N ILE C 300 " --> pdb=" O ASN C 514 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 328 through 332 removed outlier: 4.762A pdb=" N ASN C 368 " --> pdb=" O GLU C 490 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU C 490 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 622 through 625 removed outlier: 4.778A pdb=" N GLY C 568 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL C 571 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLN C 288 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR C 573 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE C 286 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLY C 575 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LYS C 284 " --> pdb=" O GLY C 575 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 665 through 670 removed outlier: 6.441A pdb=" N ALA C 646 " --> pdb=" O PRO C 639 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 685 through 689 Processing sheet with id= AM, first strand: chain 'C' and resid 691 through 702 removed outlier: 6.061A pdb=" N TYR C1041 " --> pdb=" O HIS C1022 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N HIS C1022 " --> pdb=" O TYR C1041 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 707 through 710 removed outlier: 4.324A pdb=" N LYS C 707 " --> pdb=" O LEU C 835 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 1055 through 1057 Processing sheet with id= AP, first strand: chain 'C' and resid 1068 through 1071 818 hydrogen bonds defined for protein. 2256 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: 10.21 Time building geometry restraints manager: 10.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 23772 1.54 - 1.86: 314 1.86 - 2.18: 1 2.18 - 2.51: 0 2.51 - 2.83: 1 Bond restraints: 24088 Sorted by residual: bond pdb=" C CYS A 498 " pdb=" N GLY A 499 " ideal model delta sigma weight residual 1.330 2.829 -1.498 1.49e-02 4.50e+03 1.01e+04 bond pdb=" C LEU A 308 " pdb=" N CYS A 309 " ideal model delta sigma weight residual 1.331 1.991 -0.660 2.07e-02 2.33e+03 1.02e+03 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sigma weight residual 1.410 1.475 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " ideal model delta sigma weight residual 1.528 1.589 -0.061 2.00e-02 2.50e+03 9.41e+00 ... (remaining 24083 not shown) Histogram of bond angle deviations from ideal: 88.10 - 98.50: 6 98.50 - 108.91: 1690 108.91 - 119.31: 18567 119.31 - 129.72: 12476 129.72 - 140.13: 79 Bond angle restraints: 32818 Sorted by residual: angle pdb=" O LEU A 308 " pdb=" C LEU A 308 " pdb=" N CYS A 309 " ideal model delta sigma weight residual 122.81 90.99 31.82 1.42e+00 4.96e-01 5.02e+02 angle pdb=" C CYS A 498 " pdb=" N GLY A 499 " pdb=" CA GLY A 499 " ideal model delta sigma weight residual 121.87 88.10 33.77 1.57e+00 4.06e-01 4.63e+02 angle pdb=" CA LEU A 308 " pdb=" C LEU A 308 " pdb=" N CYS A 309 " ideal model delta sigma weight residual 115.54 140.13 -24.59 1.52e+00 4.33e-01 2.62e+02 angle pdb=" O CYS A 498 " pdb=" C CYS A 498 " pdb=" N GLY A 499 " ideal model delta sigma weight residual 123.24 108.38 14.86 1.23e+00 6.61e-01 1.46e+02 angle pdb=" O1 NAG W 2 " pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 108.68 135.04 -26.36 3.00e+00 1.11e-01 7.72e+01 ... (remaining 32813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.06: 14607 23.06 - 46.13: 821 46.13 - 69.19: 156 69.19 - 92.25: 94 92.25 - 115.32: 50 Dihedral angle restraints: 15728 sinusoidal: 7398 harmonic: 8330 Sorted by residual: dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 563 " pdb=" CB CYS A 563 " ideal model delta sinusoidal sigma weight residual -86.00 -10.58 -75.42 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS C 636 " pdb=" SG CYS C 636 " pdb=" SG CYS C 645 " pdb=" CB CYS C 645 " ideal model delta sinusoidal sigma weight residual -86.00 -13.25 -72.75 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS C 512 " pdb=" SG CYS C 512 " pdb=" SG CYS C 564 " pdb=" CB CYS C 564 " ideal model delta sinusoidal sigma weight residual -86.00 -153.68 67.68 1 1.00e+01 1.00e-02 5.95e+01 ... (remaining 15725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.030: 4060 1.030 - 2.060: 8 2.060 - 3.091: 0 3.091 - 4.121: 1 4.121 - 5.151: 2 Chirality restraints: 4071 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O1 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 2.75 -5.15 2.00e-02 2.50e+03 6.63e+04 chirality pdb=" C1 NAG C1302 " pdb=" C2 NAG C1302 " pdb=" O1 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False 2.31 -2.43 4.74 2.00e-01 2.50e+01 5.62e+02 chirality pdb=" C1 NAG W 2 " pdb=" C2 NAG W 2 " pdb=" O1 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False 2.31 -1.09 3.40 2.00e-01 2.50e+01 2.90e+02 ... (remaining 4068 not shown) Planarity restraints: 4120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 139 " 0.177 2.00e-02 2.50e+03 1.72e-01 3.68e+02 pdb=" CG ASN C 139 " -0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN C 139 " -0.058 2.00e-02 2.50e+03 pdb=" ND2 ASN C 139 " -0.261 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 775 " 0.152 2.00e-02 2.50e+03 1.46e-01 2.65e+02 pdb=" CG ASN C 775 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN C 775 " -0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN C 775 " -0.221 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 256 " 0.106 2.00e-02 2.50e+03 1.26e-01 1.97e+02 pdb=" CG ASN C 256 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN C 256 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 256 " -0.205 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.154 2.00e-02 2.50e+03 ... (remaining 4117 not shown) Histogram of nonbonded interaction distances: 0.01 - 0.99: 41 0.99 - 1.97: 133 1.97 - 2.94: 11821 2.94 - 3.92: 61618 3.92 - 4.90: 114567 Warning: very small nonbonded interaction distances. Nonbonded interactions: 188180 Sorted by model distance: nonbonded pdb=" O4 NAG I 1 " pdb=" O1 NAG I 2 " model vdw 0.012 2.440 nonbonded pdb=" O4 NAG N 1 " pdb=" O1 NAG N 2 " model vdw 0.015 2.440 nonbonded pdb=" O4 NAG c 1 " pdb=" O1 NAG c 2 " model vdw 0.023 2.440 nonbonded pdb=" O4 NAG Z 1 " pdb=" O1 NAG Z 2 " model vdw 0.027 2.440 nonbonded pdb=" O4 NAG Y 1 " pdb=" O1 NAG Y 2 " model vdw 0.031 2.440 ... (remaining 188175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 39 or resid 55 through 104 or resid 138 through \ 145 or resid 162 through 214 or resid 238 through 415 or resid 433 through 443 o \ r resid 483 through 593 or resid 614 through 801 or resid 827 through 1119 or re \ sid 1306)) selection = (chain 'B' and (resid 2 through 90 or resid 97 through 104 or resid 106 through \ 158 or resid 161 through 338 or resid 345 through 355 or resid 361 through 471 o \ r resid 474 through 649 or resid 651 through 943 or resid 1104)) selection = (chain 'C' and (resid 2 through 105 or resid 139 through 146 or resid 163 throug \ h 215 or resid 239 through 416 or resid 434 through 1120 or resid 1301)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'R' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.630 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: 17.550 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 65.670 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 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 : 0.013 1.498 24088 Z= 0.861 Angle : 0.920 33.774 32818 Z= 0.467 Chirality : 0.153 5.151 4071 Planarity : 0.005 0.104 4075 Dihedral : 16.892 115.315 10239 Min Nonbonded Distance : 0.012 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.52 % Allowed : 5.46 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 2793 helix: 0.57 (0.19), residues: 661 sheet: -0.18 (0.19), residues: 640 loop : -1.37 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 860 HIS 0.005 0.001 HIS B 488 PHE 0.037 0.002 PHE B 410 TYR 0.025 0.002 TYR C1041 ARG 0.013 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 331 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 342 average time/residue: 0.3955 time to fit residues: 206.0185 Evaluate side-chains 170 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 165 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 591 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.3980 chunk 216 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 258 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 529 ASN A 536 GLN A 537 GLN A 617 GLN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 GLN A 735 GLN A 777 GLN A 874 GLN A 887 ASN A1009 GLN A1061 HIS A1079 GLN A1108 ASN B 128 ASN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN B 415 GLN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 GLN B 868 GLN B 898 HIS B 916 ASN C 396 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 758 GLN C 761 GLN C 887 GLN ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN C 927 ASN C 929 ASN C 976 GLN C 985 GLN C1032 HIS C1045 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24088 Z= 0.229 Angle : 0.893 21.677 32818 Z= 0.379 Chirality : 0.115 4.875 4071 Planarity : 0.004 0.042 4075 Dihedral : 13.690 133.648 5149 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.43 % Allowed : 11.75 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 2795 helix: 1.47 (0.20), residues: 655 sheet: -0.05 (0.19), residues: 632 loop : -1.18 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 38 HIS 0.007 0.001 HIS C1075 PHE 0.019 0.002 PHE B 29 TYR 0.023 0.001 TYR C1041 ARG 0.009 0.001 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 491 LEU cc_start: 0.6382 (mt) cc_final: 0.6124 (mt) outliers start: 36 outliers final: 16 residues processed: 211 average time/residue: 0.3543 time to fit residues: 122.0238 Evaluate side-chains 164 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 636 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 0.0170 chunk 80 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 176 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 208 optimal weight: 6.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 307 ASN A 423 ASN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 927 ASN C 976 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24088 Z= 0.207 Angle : 0.752 21.408 32818 Z= 0.328 Chirality : 0.113 4.825 4071 Planarity : 0.004 0.043 4075 Dihedral : 9.842 131.249 5149 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.99 % Allowed : 13.59 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2795 helix: 1.92 (0.20), residues: 648 sheet: 0.12 (0.19), residues: 617 loop : -1.03 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 409 HIS 0.004 0.001 HIS A 39 PHE 0.015 0.001 PHE B 155 TYR 0.023 0.001 TYR B 102 ARG 0.007 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 167 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 23 residues processed: 208 average time/residue: 0.3270 time to fit residues: 112.4757 Evaluate side-chains 165 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 1014 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 0.7980 chunk 194 optimal weight: 0.0670 chunk 134 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN A 908 GLN B 464 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 GLN ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN C 976 GLN C1075 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24088 Z= 0.220 Angle : 0.730 22.380 32818 Z= 0.318 Chirality : 0.112 4.842 4071 Planarity : 0.004 0.087 4075 Dihedral : 8.838 130.984 5143 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.23 % Allowed : 14.18 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 2795 helix: 2.05 (0.20), residues: 654 sheet: 0.21 (0.19), residues: 616 loop : -0.97 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 409 HIS 0.004 0.001 HIS A 39 PHE 0.017 0.001 PHE B 155 TYR 0.017 0.001 TYR B 864 ARG 0.005 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 147 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 34 residues processed: 196 average time/residue: 0.3090 time to fit residues: 103.6023 Evaluate side-chains 170 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 1110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 235 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24088 Z= 0.204 Angle : 0.708 22.175 32818 Z= 0.308 Chirality : 0.111 4.835 4071 Planarity : 0.004 0.073 4075 Dihedral : 8.417 135.230 5143 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.63 % Allowed : 14.90 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2795 helix: 2.15 (0.21), residues: 654 sheet: 0.22 (0.19), residues: 617 loop : -0.93 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 409 HIS 0.003 0.001 HIS A 39 PHE 0.012 0.001 PHE B 29 TYR 0.017 0.001 TYR B 864 ARG 0.004 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 147 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 41 residues processed: 204 average time/residue: 0.3069 time to fit residues: 107.4593 Evaluate side-chains 186 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 1014 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 275 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24088 Z= 0.200 Angle : 0.705 22.164 32818 Z= 0.307 Chirality : 0.111 4.843 4071 Planarity : 0.003 0.053 4075 Dihedral : 8.146 139.232 5143 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.35 % Allowed : 15.78 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2795 helix: 2.11 (0.20), residues: 653 sheet: 0.27 (0.20), residues: 609 loop : -0.90 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 409 HIS 0.003 0.001 HIS C1062 PHE 0.016 0.001 PHE B 155 TYR 0.017 0.001 TYR B 864 ARG 0.005 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 153 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 42 residues processed: 199 average time/residue: 0.3070 time to fit residues: 103.2657 Evaluate side-chains 186 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1104 ILE Chi-restraints excluded: chain C residue 1110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 157 optimal weight: 0.2980 chunk 201 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 274 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 GLN C 976 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24088 Z= 0.195 Angle : 0.706 22.013 32818 Z= 0.308 Chirality : 0.111 4.833 4071 Planarity : 0.003 0.057 4075 Dihedral : 7.982 141.422 5143 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.31 % Allowed : 16.33 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2795 helix: 2.16 (0.21), residues: 654 sheet: 0.34 (0.20), residues: 619 loop : -0.87 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 409 HIS 0.003 0.001 HIS A 39 PHE 0.017 0.001 PHE C 539 TYR 0.017 0.001 TYR B 864 ARG 0.004 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 154 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 436 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5893 (pp) outliers start: 58 outliers final: 46 residues processed: 200 average time/residue: 0.3460 time to fit residues: 116.8688 Evaluate side-chains 189 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 0.0870 chunk 82 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 174 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 135 optimal weight: 0.3980 chunk 25 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 249 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24088 Z= 0.172 Angle : 0.696 22.154 32818 Z= 0.303 Chirality : 0.111 4.852 4071 Planarity : 0.003 0.058 4075 Dihedral : 7.858 142.921 5143 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.27 % Allowed : 16.57 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2795 helix: 2.20 (0.21), residues: 654 sheet: 0.40 (0.20), residues: 621 loop : -0.86 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 63 HIS 0.003 0.000 HIS A 39 PHE 0.032 0.001 PHE B 111 TYR 0.017 0.001 TYR B 701 ARG 0.003 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 153 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 44 residues processed: 198 average time/residue: 0.3318 time to fit residues: 111.3354 Evaluate side-chains 189 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 145 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 730 TYR Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1104 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 2.9990 chunk 240 optimal weight: 0.0970 chunk 255 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 GLN C 181 HIS ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24088 Z= 0.310 Angle : 0.747 21.861 32818 Z= 0.331 Chirality : 0.110 4.829 4071 Planarity : 0.004 0.055 4075 Dihedral : 7.976 143.339 5143 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.19 % Allowed : 16.89 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2795 helix: 2.09 (0.21), residues: 658 sheet: 0.30 (0.19), residues: 638 loop : -0.84 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 63 HIS 0.004 0.001 HIS C1062 PHE 0.022 0.001 PHE B 366 TYR 0.022 0.001 TYR B 701 ARG 0.004 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 141 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 753 GLU cc_start: 0.5459 (mt-10) cc_final: 0.5216 (mt-10) outliers start: 55 outliers final: 45 residues processed: 186 average time/residue: 0.3237 time to fit residues: 101.4663 Evaluate side-chains 181 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 136 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1104 ILE Chi-restraints excluded: chain C residue 1110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 283 optimal weight: 0.1980 chunk 261 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 240 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 GLN ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24088 Z= 0.216 Angle : 0.720 21.903 32818 Z= 0.317 Chirality : 0.111 4.838 4071 Planarity : 0.003 0.054 4075 Dihedral : 7.887 144.322 5141 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.91 % Allowed : 17.17 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2795 helix: 2.10 (0.21), residues: 657 sheet: 0.37 (0.19), residues: 631 loop : -0.81 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 63 HIS 0.003 0.001 HIS C1062 PHE 0.018 0.001 PHE B 366 TYR 0.026 0.001 TYR B 701 ARG 0.004 0.000 ARG A 330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 45 residues processed: 182 average time/residue: 0.3278 time to fit residues: 99.1868 Evaluate side-chains 185 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 140 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 776 ASP Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1104 ILE Chi-restraints excluded: chain C residue 1110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 0.0370 chunk 208 optimal weight: 0.7980 chunk 33 optimal weight: 0.0020 chunk 62 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 28 optimal weight: 0.0170 chunk 41 optimal weight: 5.9990 chunk 198 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 overall best weight: 0.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 GLN ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.096816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.064126 restraints weight = 68752.610| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.73 r_work: 0.3011 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24088 Z= 0.166 Angle : 0.707 21.859 32818 Z= 0.309 Chirality : 0.111 4.826 4071 Planarity : 0.003 0.054 4075 Dihedral : 7.618 145.373 5141 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.79 % Allowed : 17.45 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2795 helix: 2.23 (0.21), residues: 646 sheet: 0.42 (0.19), residues: 643 loop : -0.81 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 63 HIS 0.003 0.000 HIS A 39 PHE 0.018 0.001 PHE B 366 TYR 0.030 0.001 TYR B 701 ARG 0.003 0.000 ARG C1081 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4567.53 seconds wall clock time: 86 minutes 18.82 seconds (5178.82 seconds total)