Starting phenix.real_space_refine (version: dev) on Fri Feb 24 18:25:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/02_2023/6zp5_11336_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/02_2023/6zp5_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_11336/02_2023/6zp5_11336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/02_2023/6zp5_11336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/02_2023/6zp5_11336_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp5_11336/02_2023/6zp5_11336_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 14.04, per 1000 atoms: 0.59 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: 11.46 Conformation dependent library (CDL) restraints added in 3.4 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: 3.91 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: 9.88 Time building geometry restraints manager: 12.13 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 G 2 " pdb=" O1 NAG G 2 " ideal model delta sigma weight residual 1.390 1.431 -0.041 1.00e-02 1.00e+04 1.68e+01 bond pdb=" C1 NAG c 2 " pdb=" O1 NAG c 2 " ideal model delta sigma weight residual 1.390 1.431 -0.041 1.00e-02 1.00e+04 1.65e+01 bond pdb=" C1 NAG B1105 " pdb=" O1 NAG B1105 " ideal model delta sigma weight residual 1.390 1.431 -0.041 1.00e-02 1.00e+04 1.65e+01 ... (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 110.25 135.04 -24.79 2.76e+00 1.32e-01 8.09e+01 ... (remaining 32813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.34: 13371 22.34 - 44.68: 762 44.68 - 67.02: 80 67.02 - 89.36: 28 89.36 - 111.69: 4 Dihedral angle restraints: 14245 sinusoidal: 5915 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 14242 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 2.30 -2.43 4.74 2.00e-01 2.50e+01 5.61e+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 2.30 -1.09 3.40 2.00e-01 2.50e+01 2.89e+02 ... (remaining 4068 not shown) Planarity restraints: 4123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O DMS A1308 " -0.204 2.00e-02 2.50e+03 2.77e-01 7.69e+02 pdb=" C1 DMS A1308 " -0.137 2.00e-02 2.50e+03 pdb=" C2 DMS A1308 " -0.137 2.00e-02 2.50e+03 pdb=" S DMS A1308 " 0.478 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O DMS A1309 " 0.201 2.00e-02 2.50e+03 2.76e-01 7.59e+02 pdb=" C1 DMS A1309 " 0.137 2.00e-02 2.50e+03 pdb=" C2 DMS A1309 " 0.137 2.00e-02 2.50e+03 pdb=" S DMS A1309 " -0.475 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O DMS A1310 " 0.173 2.00e-02 2.50e+03 2.40e-01 5.77e+02 pdb=" C1 DMS A1310 " 0.122 2.00e-02 2.50e+03 pdb=" C2 DMS A1310 " 0.119 2.00e-02 2.50e+03 pdb=" S DMS A1310 " -0.415 2.00e-02 2.50e+03 ... (remaining 4120 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 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. 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: 4.910 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: 18.190 Check model and map are aligned: 0.350 Process input model: 67.240 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 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 : 0.012 1.498 24088 Z= 0.835 Angle : 0.834 33.774 32818 Z= 0.471 Chirality : 0.152 5.151 4071 Planarity : 0.009 0.277 4078 Dihedral : 13.520 111.694 8756 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 % 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 *********************** 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 : 2.701 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: 0.3980 time to fit residues: 208.8057 Evaluate side-chains 170 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 165 time to evaluate : 2.823 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2119 time to fit residues: 5.5184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6380 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.128 24088 Z= 0.273 Angle : 0.803 21.180 32818 Z= 0.405 Chirality : 0.118 4.832 4071 Planarity : 0.004 0.038 4078 Dihedral : 7.368 100.194 3658 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.35 % 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: -0.43 (0.15), residues: 2795 helix: 1.46 (0.20), residues: 655 sheet: -0.05 (0.19), residues: 631 loop : -1.20 (0.15), residues: 1509 *********************** 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: 34 poor density : 183 time to evaluate : 2.822 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 outliers start: 34 outliers final: 15 residues processed: 211 average time/residue: 0.3495 time to fit residues: 119.3250 Evaluate side-chains 157 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 2.705 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 15 average time/residue: 0.2196 time to fit residues: 9.7947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN A 984 GLN B 230 ASN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 C1045 GLN C1075 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.155 24088 Z= 0.351 Angle : 0.756 20.978 32818 Z= 0.372 Chirality : 0.114 4.758 4071 Planarity : 0.004 0.049 4078 Dihedral : 6.650 112.899 3658 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 2.11 % 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: -0.19 (0.15), residues: 2795 helix: 1.80 (0.20), residues: 650 sheet: -0.10 (0.19), residues: 647 loop : -1.02 (0.15), residues: 1498 *********************** 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 202 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 149 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 20 residues processed: 193 average time/residue: 0.3248 time to fit residues: 105.8083 Evaluate side-chains 154 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 2.818 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.2299 time to fit residues: 12.3778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 260 optimal weight: 0.5980 chunk 275 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** 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 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.143 24088 Z= 0.241 Angle : 0.702 20.130 32818 Z= 0.343 Chirality : 0.114 4.765 4071 Planarity : 0.004 0.039 4078 Dihedral : 6.437 110.613 3658 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 2.07 % 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: -0.02 (0.15), residues: 2795 helix: 1.99 (0.20), residues: 657 sheet: 0.13 (0.19), residues: 622 loop : -1.01 (0.15), residues: 1516 *********************** 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 201 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 149 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 23 residues processed: 198 average time/residue: 0.3399 time to fit residues: 115.2242 Evaluate side-chains 158 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 2.817 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 2 residues processed: 23 average time/residue: 0.2314 time to fit residues: 13.9723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 0.3980 chunk 156 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 113 optimal weight: 0.0050 chunk 235 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 247 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 777 GLN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.145 24088 Z= 0.199 Angle : 0.690 20.321 32818 Z= 0.334 Chirality : 0.114 4.765 4071 Planarity : 0.003 0.043 4078 Dihedral : 6.300 109.459 3658 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.59 % 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: 0.08 (0.15), residues: 2795 helix: 2.10 (0.20), residues: 656 sheet: 0.24 (0.20), residues: 608 loop : -0.97 (0.15), residues: 1531 *********************** 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 186 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 146 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 18 residues processed: 179 average time/residue: 0.3231 time to fit residues: 98.2186 Evaluate side-chains 153 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 2.609 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 18 average time/residue: 0.2217 time to fit residues: 11.1195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 275 optimal weight: 0.5980 chunk 228 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 GLN C 976 GLN C1045 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.146 24088 Z= 0.215 Angle : 0.688 20.346 32818 Z= 0.333 Chirality : 0.114 4.764 4071 Planarity : 0.003 0.046 4078 Dihedral : 6.226 108.299 3658 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.08 % 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: 2.16 (0.20), residues: 654 sheet: 0.28 (0.20), residues: 609 loop : -0.93 (0.15), residues: 1532 *********************** 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 175 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 167 average time/residue: 0.3396 time to fit residues: 96.0270 Evaluate side-chains 153 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 3.053 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.2199 time to fit residues: 9.3014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 99 ASN ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.145 24088 Z= 0.315 Angle : 0.721 20.616 32818 Z= 0.351 Chirality : 0.113 4.768 4071 Planarity : 0.004 0.049 4078 Dihedral : 6.291 107.397 3658 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2795 helix: 2.01 (0.21), residues: 665 sheet: 0.18 (0.19), residues: 649 loop : -0.91 (0.15), residues: 1481 *********************** 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 167 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 160 average time/residue: 0.3345 time to fit residues: 90.1127 Evaluate side-chains 149 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 2.869 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 17 average time/residue: 0.2244 time to fit residues: 11.0878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 249 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 181 HIS ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.142 24088 Z= 0.222 Angle : 0.694 20.854 32818 Z= 0.335 Chirality : 0.114 4.794 4071 Planarity : 0.003 0.049 4078 Dihedral : 6.197 106.687 3658 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.60 % 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: 0.16 (0.16), residues: 2795 helix: 2.08 (0.21), residues: 663 sheet: 0.27 (0.19), residues: 637 loop : -0.89 (0.15), residues: 1495 *********************** 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 162 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 160 average time/residue: 0.3347 time to fit residues: 89.9982 Evaluate side-chains 141 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 2.796 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.2251 time to fit residues: 7.1965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 255 optimal weight: 0.0470 chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 270 optimal weight: 2.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- 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 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.145 24088 Z= 0.251 Angle : 0.699 20.717 32818 Z= 0.339 Chirality : 0.113 4.771 4071 Planarity : 0.003 0.052 4078 Dihedral : 6.198 106.602 3658 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.56 % 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: 0.18 (0.16), residues: 2795 helix: 2.06 (0.21), residues: 665 sheet: 0.32 (0.20), residues: 636 loop : -0.89 (0.15), residues: 1494 *********************** 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 152 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 146 average time/residue: 0.3574 time to fit residues: 88.2798 Evaluate side-chains 141 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 3.010 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.2397 time to fit residues: 7.0324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 188 optimal weight: 0.7980 chunk 283 optimal weight: 0.6980 chunk 261 optimal weight: 0.1980 chunk 226 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 240 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.146 24088 Z= 0.192 Angle : 0.690 20.774 32818 Z= 0.332 Chirality : 0.114 4.778 4071 Planarity : 0.003 0.053 4078 Dihedral : 6.098 106.004 3658 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.24 % 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: 0.22 (0.16), residues: 2795 helix: 2.12 (0.21), residues: 665 sheet: 0.41 (0.20), residues: 618 loop : -0.90 (0.15), residues: 1512 ********************** 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 151 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 149 average time/residue: 0.3823 time to fit residues: 95.3521 Evaluate side-chains 138 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 2.947 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.2244 time to fit residues: 4.8615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 0.0050 chunk 208 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 226 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 975 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 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 = 0.3852 r_free = 0.3852 target = 0.095942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.063070 restraints weight = 69293.890| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.78 r_work: 0.2978 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.146 24088 Z= 0.197 Angle : 0.688 20.741 32818 Z= 0.331 Chirality : 0.113 4.773 4071 Planarity : 0.003 0.051 4078 Dihedral : 6.058 106.010 3658 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 0.24 % 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: 0.24 (0.16), residues: 2795 helix: 2.15 (0.21), residues: 665 sheet: 0.40 (0.20), residues: 630 loop : -0.88 (0.15), residues: 1500 =============================================================================== Job complete usr+sys time: 4441.21 seconds wall clock time: 84 minutes 7.35 seconds (5047.35 seconds total)