Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 19:00:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syi_40874/08_2023/8syi_40874.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syi_40874/08_2023/8syi_40874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syi_40874/08_2023/8syi_40874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syi_40874/08_2023/8syi_40874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syi_40874/08_2023/8syi_40874.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syi_40874/08_2023/8syi_40874.pdb" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.059 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 90 5.49 5 Mg 1 5.21 5 S 83 5.16 5 C 18179 2.51 5 N 5265 2.21 5 O 5880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ASP 15": "OD1" <-> "OD2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C ASP 297": "OD1" <-> "OD2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 483": "OD1" <-> "OD2" Residue "C TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 695": "OE1" <-> "OE2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 793": "OE1" <-> "OE2" Residue "C GLU 839": "OE1" <-> "OE2" Residue "C ASP 921": "OD1" <-> "OD2" Residue "C ASP 957": "OD1" <-> "OD2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D ASP 231": "OD1" <-> "OD2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D ASP 310": "OD1" <-> "OD2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 91": "OE1" <-> "OE2" Residue "Z ASP 103": "OD1" <-> "OD2" Residue "Z GLU 253": "OE1" <-> "OE2" Residue "Z ASP 270": "OD1" <-> "OD2" Residue "Z GLU 351": "OE1" <-> "OE2" Residue "Z GLU 381": "OE1" <-> "OE2" Residue "Z GLU 554": "OE1" <-> "OE2" Residue "Z ASP 692": "OD1" <-> "OD2" Residue "Z GLU 784": "OE1" <-> "OE2" Residue "Z ASP 845": "OD1" <-> "OD2" Residue "Z GLU 878": "OE1" <-> "OE2" Residue "Z ASP 930": "OD1" <-> "OD2" Residue "Z ASP 1075": "OD1" <-> "OD2" Residue "Z TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 1127": "OE1" <-> "OE2" Residue "Z ARG 1131": "NH1" <-> "NH2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E GLU 67": "OE1" <-> "OE2" Residue "G GLU 33": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 29500 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 215} Chain: "B" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 215} Chain: "C" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8382 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 59, 'TRANS': 1001} Chain breaks: 1 Chain: "D" Number of atoms: 4961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4961 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 32, 'TRANS': 587} Chain: "Z" Number of atoms: 9357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1221, 9357 Classifications: {'peptide': 1221} Link IDs: {'PTRANS': 46, 'TRANS': 1174} Chain breaks: 3 Chain: "E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 510 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "G" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 957 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "N" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 745 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "R" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 370 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 11} Chain: "T" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 755 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12382 SG CYS D 70 48.424 127.240 97.226 1.00112.12 S ATOM 12398 SG CYS D 72 49.973 130.156 95.264 1.00112.11 S ATOM 12507 SG CYS D 85 46.233 129.492 95.178 1.00111.11 S ATOM 12533 SG CYS D 88 48.800 126.998 93.578 1.00113.28 S ATOM 18529 SG CYS Z 221 27.316 71.459 132.195 1.00 49.30 S ATOM 19085 SG CYS Z 295 30.483 72.129 129.972 1.00 35.82 S ATOM 19134 SG CYS Z 302 29.859 73.750 133.373 1.00 39.95 S ATOM 19158 SG CYS Z 305 30.803 70.217 133.314 1.00 49.73 S Time building chain proxies: 15.19, per 1000 atoms: 0.51 Number of scatterers: 29500 At special positions: 0 Unit cell: (139.2, 146.16, 215.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 83 16.00 P 90 15.00 Mg 1 11.99 O 5880 8.00 N 5265 7.00 C 18179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.76 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 85 " pdb=" ZN Z1401 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 302 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 221 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 305 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 295 " Number of angles added : 12 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6516 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 54 sheets defined 30.5% alpha, 17.6% beta 33 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 9.95 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 removed outlier: 4.078A pdb=" N THR A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.817A pdb=" N ASN A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 204 through 221 Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.685A pdb=" N THR B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 206 through 221 removed outlier: 3.619A pdb=" N ALA B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 219 " --> pdb=" O CYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.652A pdb=" N GLU C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 182 through 189 Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.594A pdb=" N ILE C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 200 " --> pdb=" O ILE C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 4.099A pdb=" N TYR C 206 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 230 Processing helix chain 'C' and resid 236 through 248 Processing helix chain 'C' and resid 256 through 269 removed outlier: 3.685A pdb=" N GLY C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 297 removed outlier: 3.698A pdb=" N ILE C 284 " --> pdb=" O THR C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 341 removed outlier: 4.044A pdb=" N THR C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 356 through 370 removed outlier: 3.910A pdb=" N SER C 370 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 388 removed outlier: 3.839A pdb=" N LYS C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 removed outlier: 4.008A pdb=" N TYR C 416 " --> pdb=" O PRO C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.726A pdb=" N ASP C 475 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP C 476 " --> pdb=" O GLN C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 472 through 476' Processing helix chain 'C' and resid 527 through 531 removed outlier: 3.640A pdb=" N LEU C 530 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 531 " --> pdb=" O THR C 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 527 through 531' Processing helix chain 'C' and resid 533 through 537 Processing helix chain 'C' and resid 538 through 549 Processing helix chain 'C' and resid 567 through 572 removed outlier: 3.552A pdb=" N ALA C 572 " --> pdb=" O GLU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 681 removed outlier: 3.517A pdb=" N TYR C 680 " --> pdb=" O GLU C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 718 Processing helix chain 'C' and resid 855 through 859 removed outlier: 3.719A pdb=" N GLY C 858 " --> pdb=" O ASN C 855 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 859 " --> pdb=" O PRO C 856 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 855 through 859' Processing helix chain 'C' and resid 865 through 881 removed outlier: 3.719A pdb=" N PHE C 869 " --> pdb=" O VAL C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 914 removed outlier: 3.510A pdb=" N LEU C 900 " --> pdb=" O GLU C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 919 removed outlier: 3.516A pdb=" N VAL C 918 " --> pdb=" O GLN C 915 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 919 " --> pdb=" O PRO C 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 915 through 919' Processing helix chain 'C' and resid 955 through 959 Processing helix chain 'C' and resid 978 through 982 removed outlier: 3.785A pdb=" N GLN C 982 " --> pdb=" O LYS C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 998 Processing helix chain 'C' and resid 1001 through 1009 Processing helix chain 'C' and resid 1016 through 1028 removed outlier: 3.565A pdb=" N GLU C1020 " --> pdb=" O GLN C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1049 removed outlier: 3.910A pdb=" N LYS C1041 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 25 removed outlier: 3.705A pdb=" N GLY D 25 " --> pdb=" O ILE D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.540A pdb=" N PHE D 62 " --> pdb=" O CYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.774A pdb=" N VAL D 97 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 162 through 174 removed outlier: 3.609A pdb=" N GLN D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 200 through 214 removed outlier: 4.018A pdb=" N GLU D 214 " --> pdb=" O GLN D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 237 Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 270 through 292 removed outlier: 3.560A pdb=" N LEU D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 314 removed outlier: 3.823A pdb=" N ASN D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 339 removed outlier: 4.529A pdb=" N GLY D 339 " --> pdb=" O ASP D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 348 removed outlier: 3.613A pdb=" N LEU D 348 " --> pdb=" O PHE D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 383 removed outlier: 3.760A pdb=" N ILE D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU D 381 " --> pdb=" O GLU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 394 Processing helix chain 'D' and resid 399 through 410 Processing helix chain 'D' and resid 412 through 422 removed outlier: 3.844A pdb=" N ASP D 416 " --> pdb=" O PRO D 412 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 438 No H-bonds generated for 'chain 'D' and resid 436 through 438' Processing helix chain 'D' and resid 456 through 458 No H-bonds generated for 'chain 'D' and resid 456 through 458' Processing helix chain 'D' and resid 459 through 464 Processing helix chain 'D' and resid 479 through 490 Processing helix chain 'D' and resid 491 through 495 removed outlier: 4.063A pdb=" N ASN D 495 " --> pdb=" O ALA D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 521 removed outlier: 3.989A pdb=" N LEU D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 546 removed outlier: 3.850A pdb=" N ALA D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 608 through 624 Processing helix chain 'Z' and resid 16 through 32 removed outlier: 3.562A pdb=" N GLY Z 32 " --> pdb=" O PHE Z 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 51 removed outlier: 3.809A pdb=" N VAL Z 38 " --> pdb=" O ALA Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 89 removed outlier: 3.524A pdb=" N ARG Z 89 " --> pdb=" O ASP Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 93 through 121 removed outlier: 3.522A pdb=" N ARG Z 97 " --> pdb=" O THR Z 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE Z 98 " --> pdb=" O GLU Z 94 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN Z 99 " --> pdb=" O VAL Z 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP Z 105 " --> pdb=" O VAL Z 101 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN Z 109 " --> pdb=" O TRP Z 105 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP Z 110 " --> pdb=" O ALA Z 106 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 135 Processing helix chain 'Z' and resid 144 through 149 Processing helix chain 'Z' and resid 175 through 211 removed outlier: 3.740A pdb=" N ILE Z 180 " --> pdb=" O VAL Z 176 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE Z 181 " --> pdb=" O THR Z 177 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY Z 185 " --> pdb=" O ILE Z 181 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR Z 197 " --> pdb=" O THR Z 193 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ALA Z 198 " --> pdb=" O ALA Z 194 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP Z 199 " --> pdb=" O LEU Z 195 " (cutoff:3.500A) Processing helix chain 'Z' and resid 241 through 246 removed outlier: 3.570A pdb=" N ARG Z 245 " --> pdb=" O PRO Z 241 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 282 Processing helix chain 'Z' and resid 302 through 307 Processing helix chain 'Z' and resid 321 through 332 removed outlier: 3.778A pdb=" N ILE Z 325 " --> pdb=" O ALA Z 321 " (cutoff:3.500A) Processing helix chain 'Z' and resid 333 through 337 Processing helix chain 'Z' and resid 764 through 768 removed outlier: 3.880A pdb=" N SER Z 767 " --> pdb=" O GLU Z 764 " (cutoff:3.500A) Processing helix chain 'Z' and resid 807 through 811 removed outlier: 3.512A pdb=" N SER Z 811 " --> pdb=" O SER Z 808 " (cutoff:3.500A) Processing helix chain 'Z' and resid 994 through 1003 Processing helix chain 'Z' and resid 1072 through 1088 removed outlier: 3.780A pdb=" N GLU Z1078 " --> pdb=" O HIS Z1074 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1090 through 1117 removed outlier: 3.825A pdb=" N ALA Z1094 " --> pdb=" O GLU Z1090 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN Z1117 " --> pdb=" O VAL Z1113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1122 through 1131 removed outlier: 4.234A pdb=" N ILE Z1126 " --> pdb=" O SER Z1122 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE Z1129 " --> pdb=" O HIS Z1125 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1155 through 1167 Processing helix chain 'Z' and resid 1191 through 1197 removed outlier: 3.550A pdb=" N ALA Z1195 " --> pdb=" O SER Z1191 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1200 through 1212 Processing helix chain 'Z' and resid 1222 through 1227 removed outlier: 3.517A pdb=" N ILE Z1226 " --> pdb=" O GLU Z1222 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1232 through 1236 removed outlier: 3.852A pdb=" N GLY Z1235 " --> pdb=" O ALA Z1232 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 25 through 44 removed outlier: 3.926A pdb=" N VAL E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 32 " --> pdb=" O HIS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'G' and resid 33 through 48 Processing helix chain 'G' and resid 91 through 100 Processing helix chain 'G' and resid 129 through 137 removed outlier: 3.647A pdb=" N VAL G 133 " --> pdb=" O SER G 129 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 12 removed outlier: 6.758A pdb=" N ARG A 21 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER A 10 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A 19 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 18 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP A 191 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 174 " --> pdb=" O TRP A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 101 removed outlier: 7.289A pdb=" N GLU A 136 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE A 57 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU A 138 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 55 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS A 140 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 107 removed outlier: 3.855A pdb=" N VAL A 106 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 12 removed outlier: 6.762A pdb=" N ARG B 21 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER B 10 " --> pdb=" O TYR B 19 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B 19 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP B 191 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 174 " --> pdb=" O TRP B 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 98 removed outlier: 3.607A pdb=" N GLN B 94 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 141 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU B 138 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 55 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS B 140 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.582A pdb=" N ALA B 127 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.840A pdb=" N GLY C 104 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 84 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE C 102 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR C 86 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU C 100 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU C 88 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLU C 98 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN C 90 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE C 96 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 115 through 117 Processing sheet with id=AB3, first strand: chain 'C' and resid 312 through 315 removed outlier: 3.782A pdb=" N ASN C 126 " --> pdb=" O ARG C 390 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 133 through 140 removed outlier: 4.340A pdb=" N HIS C 148 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 441 through 442 Processing sheet with id=AB6, first strand: chain 'C' and resid 459 through 461 removed outlier: 4.541A pdb=" N ARG C 454 " --> pdb=" O ARG C 461 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 497 through 500 Processing sheet with id=AB8, first strand: chain 'C' and resid 563 through 564 removed outlier: 3.639A pdb=" N GLY C 564 " --> pdb=" O PHE C 884 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 579 through 580 removed outlier: 6.647A pdb=" N ILE C 579 " --> pdb=" O ILE C 639 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 604 through 608 removed outlier: 6.673A pdb=" N HIS C 594 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL C 590 " --> pdb=" O HIS C 594 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU C 596 " --> pdb=" O SER C 588 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 926 through 927 removed outlier: 7.326A pdb=" N ILE C 672 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C 835 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE C 674 " --> pdb=" O ILE C 835 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 673 " --> pdb=" O VAL C 853 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N ILE C 852 " --> pdb=" O ASN C 655 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 657 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU C 854 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA C 659 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR C 943 " --> pdb=" O TYR C 660 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 686 through 697 removed outlier: 6.419A pdb=" N SER C 686 " --> pdb=" O LYS C 813 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS C 813 " --> pdb=" O SER C 686 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N HIS C 688 " --> pdb=" O ALA C 811 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA C 811 " --> pdb=" O HIS C 688 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU C 690 " --> pdb=" O TYR C 809 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR C 809 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE C 692 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG C 807 " --> pdb=" O PHE C 692 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE C 694 " --> pdb=" O VAL C 805 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL C 805 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA C 696 " --> pdb=" O ASN C 803 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TYR C 809 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 686 through 697 removed outlier: 6.419A pdb=" N SER C 686 " --> pdb=" O LYS C 813 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS C 813 " --> pdb=" O SER C 686 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N HIS C 688 " --> pdb=" O ALA C 811 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA C 811 " --> pdb=" O HIS C 688 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU C 690 " --> pdb=" O TYR C 809 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR C 809 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE C 692 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG C 807 " --> pdb=" O PHE C 692 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE C 694 " --> pdb=" O VAL C 805 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL C 805 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA C 696 " --> pdb=" O ASN C 803 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 705 through 706 removed outlier: 3.637A pdb=" N GLU C 705 " --> pdb=" O VAL C 743 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 738 through 740 removed outlier: 7.205A pdb=" N LEU C 774 " --> pdb=" O LEU C 739 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 961 through 963 removed outlier: 6.465A pdb=" N CYS D 372 " --> pdb=" O ILE D 446 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL D 448 " --> pdb=" O CYS D 372 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU D 374 " --> pdb=" O VAL D 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 985 through 987 removed outlier: 3.818A pdb=" N GLN C 985 " --> pdb=" O VAL D 353 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1068 through 1070 removed outlier: 4.864A pdb=" N VAL C1056 " --> pdb=" O VAL C1070 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 104 through 112 removed outlier: 6.884A pdb=" N ASN D 246 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N ALA D 109 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N VAL D 244 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 160 through 161 removed outlier: 3.789A pdb=" N TYR D 144 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 185 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.807A pdb=" N VAL D 259 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 533 through 535 Processing sheet with id=AD5, first strand: chain 'D' and resid 563 through 565 Processing sheet with id=AD6, first strand: chain 'D' and resid 576 through 577 removed outlier: 3.632A pdb=" N VAL D 576 " --> pdb=" O THR D 584 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG D 593 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 227 through 229 Processing sheet with id=AD8, first strand: chain 'Z' and resid 232 through 234 removed outlier: 6.620A pdb=" N MET Z 232 " --> pdb=" O LEU Z 239 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG Z 237 " --> pdb=" O ASP Z 234 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 255 through 256 removed outlier: 6.686A pdb=" N VAL Z 255 " --> pdb=" O LEU Z 264 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 353 through 358 removed outlier: 6.329A pdb=" N ALA Z 358 " --> pdb=" O ILE Z 424 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE Z 424 " --> pdb=" O ALA Z 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 395 through 396 Processing sheet with id=AE3, first strand: chain 'Z' and resid 441 through 446 removed outlier: 4.323A pdb=" N VAL Z 979 " --> pdb=" O VAL Z 445 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Z' and resid 955 through 957 removed outlier: 3.533A pdb=" N GLY Z 451 " --> pdb=" O VAL Z 972 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 460 through 462 Processing sheet with id=AE6, first strand: chain 'Z' and resid 486 through 489 Processing sheet with id=AE7, first strand: chain 'Z' and resid 509 through 517 removed outlier: 6.712A pdb=" N VAL Z 509 " --> pdb=" O GLN Z 875 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN Z 875 " --> pdb=" O VAL Z 509 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA Z 511 " --> pdb=" O GLN Z 873 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLN Z 873 " --> pdb=" O ALA Z 511 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR Z 513 " --> pdb=" O CYS Z 871 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS Z 871 " --> pdb=" O THR Z 513 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU Z 515 " --> pdb=" O ILE Z 869 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA Z 867 " --> pdb=" O THR Z 517 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 563 through 566 Processing sheet with id=AE9, first strand: chain 'Z' and resid 603 through 605 removed outlier: 3.585A pdb=" N ILE Z 634 " --> pdb=" O LEU Z 603 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 623 through 625 removed outlier: 4.328A pdb=" N GLN Z 776 " --> pdb=" O VAL Z 625 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 638 through 639 Processing sheet with id=AF3, first strand: chain 'Z' and resid 692 through 697 removed outlier: 4.021A pdb=" N ASP Z 692 " --> pdb=" O LEU Z 742 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS Z 694 " --> pdb=" O LEU Z 740 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU Z 740 " --> pdb=" O HIS Z 694 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 903 through 904 removed outlier: 3.535A pdb=" N LEU Z 950 " --> pdb=" O VAL Z 904 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 1031 through 1032 Processing sheet with id=AF6, first strand: chain 'Z' and resid 1152 through 1154 Processing sheet with id=AF7, first strand: chain 'G' and resid 53 through 57 removed outlier: 7.827A pdb=" N ALA G 25 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE G 107 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN G 27 " --> pdb=" O ILE G 105 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 60 through 66 Processing sheet with id=AF9, first strand: chain 'G' and resid 109 through 111 959 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 13.96 Time building geometry restraints manager: 12.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7762 1.33 - 1.45: 5394 1.45 - 1.57: 16700 1.57 - 1.69: 179 1.69 - 1.82: 138 Bond restraints: 30173 Sorted by residual: bond pdb=" N GLN Z 917 " pdb=" CA GLN Z 917 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.46e+01 bond pdb=" CA GLU E 44 " pdb=" C GLU E 44 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.38e-02 5.25e+03 8.79e+00 bond pdb=" N LEU Z 916 " pdb=" CA LEU Z 916 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.18e+00 bond pdb=" N SER Z 920 " pdb=" CA SER Z 920 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.31e-02 5.83e+03 6.03e+00 bond pdb=" N GLN Z 915 " pdb=" CA GLN Z 915 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.34e+00 ... (remaining 30168 not shown) Histogram of bond angle deviations from ideal: 97.38 - 104.72: 770 104.72 - 112.07: 15060 112.07 - 119.41: 10635 119.41 - 126.75: 14261 126.75 - 134.10: 549 Bond angle restraints: 41275 Sorted by residual: angle pdb=" C ASN Z 680 " pdb=" N ASP Z 681 " pdb=" CA ASP Z 681 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C ALA D 535 " pdb=" N ASN D 536 " pdb=" CA ASN D 536 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.94e+01 angle pdb=" N ILE D 120 " pdb=" CA ILE D 120 " pdb=" C ILE D 120 " ideal model delta sigma weight residual 112.35 107.55 4.80 1.20e+00 6.94e-01 1.60e+01 angle pdb=" C HIS B 62 " pdb=" N GLU B 63 " pdb=" CA GLU B 63 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 angle pdb=" CA GLU E 44 " pdb=" CB GLU E 44 " pdb=" CG GLU E 44 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.50e+01 ... (remaining 41270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14679 17.94 - 35.88: 2267 35.88 - 53.82: 900 53.82 - 71.76: 207 71.76 - 89.70: 61 Dihedral angle restraints: 18114 sinusoidal: 7979 harmonic: 10135 Sorted by residual: dihedral pdb=" CA ILE D 120 " pdb=" C ILE D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 180.00 153.50 26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA GLU B 63 " pdb=" C GLU B 63 " pdb=" N PHE B 64 " pdb=" CA PHE B 64 " ideal model delta harmonic sigma weight residual 180.00 154.03 25.97 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA SER A 187 " pdb=" C SER A 187 " pdb=" N THR A 188 " pdb=" CA THR A 188 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 18111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3695 0.051 - 0.102: 802 0.102 - 0.153: 210 0.153 - 0.204: 4 0.204 - 0.255: 1 Chirality restraints: 4712 Sorted by residual: chirality pdb=" CA PRO Z1017 " pdb=" N PRO Z1017 " pdb=" C PRO Z1017 " pdb=" CB PRO Z1017 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLN Z 917 " pdb=" N GLN Z 917 " pdb=" C GLN Z 917 " pdb=" CB GLN Z 917 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA ARG Z1131 " pdb=" N ARG Z1131 " pdb=" C ARG Z1131 " pdb=" CB ARG Z1131 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 4709 not shown) Planarity restraints: 5119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Z1131 " -0.757 9.50e-02 1.11e+02 3.39e-01 7.00e+01 pdb=" NE ARG Z1131 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG Z1131 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG Z1131 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG Z1131 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG Z1016 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO Z1017 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO Z1017 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO Z1017 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 509 " -0.053 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO C 510 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 510 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 510 " -0.043 5.00e-02 4.00e+02 ... (remaining 5116 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 787 2.69 - 3.24: 25911 3.24 - 3.80: 42884 3.80 - 4.35: 56651 4.35 - 4.90: 97265 Nonbonded interactions: 223498 Sorted by model distance: nonbonded pdb=" O ILE D 369 " pdb=" ND1 HIS D 370 " model vdw 2.138 2.520 nonbonded pdb=" OD1 ASP D 468 " pdb="MG MG D1001 " model vdw 2.166 2.170 nonbonded pdb=" O THR Z 630 " pdb=" OG1 THR Z 630 " model vdw 2.188 2.440 nonbonded pdb=" N ASP A 73 " pdb=" OD1 ASP A 73 " model vdw 2.203 2.520 nonbonded pdb=" O3' A R 20 " pdb="MG MG D1001 " model vdw 2.209 2.170 ... (remaining 223493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.610 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: 15.920 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 89.320 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.004 0.096 30173 Z= 0.282 Angle : 0.636 9.139 41275 Z= 0.346 Chirality : 0.045 0.255 4712 Planarity : 0.007 0.339 5119 Dihedral : 20.532 89.702 11598 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.74 % Favored : 91.92 % Rotamer Outliers : 6.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3515 helix: 0.88 (0.17), residues: 938 sheet: -0.31 (0.22), residues: 547 loop : -2.26 (0.12), residues: 2030 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 264 time to evaluate : 3.670 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 outliers start: 181 outliers final: 107 residues processed: 434 average time/residue: 1.3730 time to fit residues: 700.9166 Evaluate side-chains 289 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 182 time to evaluate : 3.609 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 105 residues processed: 2 average time/residue: 0.4203 time to fit residues: 6.1538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 10.0000 chunk 272 optimal weight: 30.0000 chunk 150 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 281 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 209 optimal weight: 7.9990 chunk 326 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN C 126 ASN C 503 GLN C 826 HIS Z 649 ASN G 103 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.090 30173 Z= 0.410 Angle : 0.653 11.772 41275 Z= 0.341 Chirality : 0.045 0.344 4712 Planarity : 0.005 0.146 5119 Dihedral : 13.344 89.575 4818 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.08 % Favored : 91.61 % Rotamer Outliers : 8.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3515 helix: 1.20 (0.17), residues: 958 sheet: -0.62 (0.22), residues: 591 loop : -2.22 (0.13), residues: 1966 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 192 time to evaluate : 3.201 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 outliers start: 263 outliers final: 138 residues processed: 433 average time/residue: 1.2419 time to fit residues: 644.6225 Evaluate side-chains 314 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 176 time to evaluate : 3.517 Switching outliers to nearest non-outliers outliers start: 138 outliers final: 133 residues processed: 5 average time/residue: 0.8361 time to fit residues: 9.8523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 181 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 271 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 326 optimal weight: 5.9990 chunk 352 optimal weight: 20.0000 chunk 290 optimal weight: 9.9990 chunk 323 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 262 optimal weight: 30.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 864 ASN E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 30173 Z= 0.294 Angle : 0.601 12.485 41275 Z= 0.313 Chirality : 0.044 0.344 4712 Planarity : 0.005 0.143 5119 Dihedral : 13.282 89.866 4818 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.68 % Favored : 92.03 % Rotamer Outliers : 8.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3515 helix: 1.42 (0.18), residues: 956 sheet: -0.53 (0.22), residues: 592 loop : -2.14 (0.13), residues: 1967 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 175 time to evaluate : 3.111 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 outliers start: 242 outliers final: 152 residues processed: 394 average time/residue: 1.1943 time to fit residues: 570.0427 Evaluate side-chains 326 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 174 time to evaluate : 3.486 Switching outliers to nearest non-outliers outliers start: 152 outliers final: 148 residues processed: 5 average time/residue: 0.7729 time to fit residues: 9.8108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 322 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 347 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 46 ASN C 126 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** Z 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 915 GLN ** Z 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 30173 Z= 0.400 Angle : 0.639 12.833 41275 Z= 0.332 Chirality : 0.046 0.348 4712 Planarity : 0.005 0.145 5119 Dihedral : 13.335 88.705 4818 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.25 % Favored : 91.47 % Rotamer Outliers : 7.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3515 helix: 1.40 (0.18), residues: 958 sheet: -0.62 (0.22), residues: 592 loop : -2.13 (0.13), residues: 1965 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 179 time to evaluate : 3.364 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 outliers start: 238 outliers final: 165 residues processed: 402 average time/residue: 1.1717 time to fit residues: 571.7608 Evaluate side-chains 329 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 164 time to evaluate : 3.442 Switching outliers to nearest non-outliers outliers start: 165 outliers final: 159 residues processed: 6 average time/residue: 0.5253 time to fit residues: 9.0612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 289 optimal weight: 50.0000 chunk 196 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 258 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 311 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** Z 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 915 GLN ** Z 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 30173 Z= 0.318 Angle : 0.611 11.211 41275 Z= 0.318 Chirality : 0.044 0.262 4712 Planarity : 0.005 0.131 5119 Dihedral : 13.311 89.540 4818 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.97 % Favored : 91.75 % Rotamer Outliers : 7.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3515 helix: 1.49 (0.18), residues: 957 sheet: -0.58 (0.22), residues: 605 loop : -2.07 (0.13), residues: 1953 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 169 time to evaluate : 3.442 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 outliers start: 230 outliers final: 175 residues processed: 380 average time/residue: 1.2036 time to fit residues: 554.2779 Evaluate side-chains 345 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 170 time to evaluate : 3.597 Switching outliers to nearest non-outliers outliers start: 175 outliers final: 166 residues processed: 10 average time/residue: 0.7053 time to fit residues: 14.2896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 116 optimal weight: 4.9990 chunk 312 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 347 optimal weight: 9.9990 chunk 288 optimal weight: 50.0000 chunk 160 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** Z 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 886 GLN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 30173 Z= 0.273 Angle : 0.601 16.284 41275 Z= 0.310 Chirality : 0.043 0.345 4712 Planarity : 0.005 0.159 5119 Dihedral : 13.257 89.364 4818 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.68 % Favored : 92.01 % Rotamer Outliers : 7.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3515 helix: 1.60 (0.18), residues: 955 sheet: -0.58 (0.22), residues: 603 loop : -1.99 (0.13), residues: 1957 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 171 time to evaluate : 3.274 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: 234 outliers final: 175 residues processed: 383 average time/residue: 1.1821 time to fit residues: 551.1916 Evaluate side-chains 346 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 171 time to evaluate : 3.304 Switching outliers to nearest non-outliers outliers start: 175 outliers final: 167 residues processed: 9 average time/residue: 0.6792 time to fit residues: 12.8608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 334 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 253 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 292 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 346 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** Z 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 30173 Z= 0.211 Angle : 0.586 12.034 41275 Z= 0.302 Chirality : 0.042 0.287 4712 Planarity : 0.004 0.140 5119 Dihedral : 13.184 89.092 4818 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.11 % Favored : 92.60 % Rotamer Outliers : 7.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.89 (0.14), residues: 3515 helix: 1.73 (0.18), residues: 953 sheet: -0.44 (0.22), residues: 608 loop : -1.95 (0.13), residues: 1954 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 166 time to evaluate : 3.595 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: 214 outliers final: 163 residues processed: 364 average time/residue: 1.2056 time to fit residues: 532.0764 Evaluate side-chains 328 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 165 time to evaluate : 3.282 Switching outliers to nearest non-outliers outliers start: 163 outliers final: 156 residues processed: 9 average time/residue: 0.8473 time to fit residues: 14.6151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 214 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 206 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 314 optimal weight: 0.6980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN C 864 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** Z 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 30173 Z= 0.417 Angle : 0.663 20.955 41275 Z= 0.341 Chirality : 0.045 0.364 4712 Planarity : 0.005 0.173 5119 Dihedral : 13.323 88.249 4818 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.59 % Favored : 91.12 % Rotamer Outliers : 7.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3515 helix: 1.52 (0.18), residues: 955 sheet: -0.52 (0.22), residues: 620 loop : -1.99 (0.13), residues: 1940 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 164 time to evaluate : 3.816 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 outliers start: 212 outliers final: 164 residues processed: 358 average time/residue: 1.2104 time to fit residues: 526.8196 Evaluate side-chains 322 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 158 time to evaluate : 3.190 Switching outliers to nearest non-outliers outliers start: 164 outliers final: 159 residues processed: 7 average time/residue: 0.7241 time to fit residues: 11.2275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 331 optimal weight: 0.9980 chunk 302 optimal weight: 10.0000 chunk 322 optimal weight: 3.9990 chunk 194 optimal weight: 0.0870 chunk 140 optimal weight: 0.7980 chunk 253 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 291 optimal weight: 50.0000 chunk 304 optimal weight: 6.9990 chunk 321 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** Z 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 30173 Z= 0.179 Angle : 0.601 16.561 41275 Z= 0.310 Chirality : 0.042 0.337 4712 Planarity : 0.005 0.156 5119 Dihedral : 13.206 89.623 4818 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.00 % Favored : 92.75 % Rotamer Outliers : 6.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.83 (0.14), residues: 3515 helix: 1.74 (0.18), residues: 953 sheet: -0.35 (0.22), residues: 613 loop : -1.91 (0.13), residues: 1949 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 165 time to evaluate : 3.285 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: 181 outliers final: 159 residues processed: 338 average time/residue: 1.2263 time to fit residues: 503.8405 Evaluate side-chains 317 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 158 time to evaluate : 3.305 Switching outliers to nearest non-outliers outliers start: 159 outliers final: 155 residues processed: 5 average time/residue: 0.6884 time to fit residues: 9.3737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 340 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 161 optimal weight: 0.0970 chunk 237 optimal weight: 0.0170 chunk 357 optimal weight: 4.9990 chunk 329 optimal weight: 4.9990 chunk 284 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 174 optimal weight: 0.0980 chunk 226 optimal weight: 3.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** Z 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 30173 Z= 0.186 Angle : 0.608 14.541 41275 Z= 0.310 Chirality : 0.042 0.303 4712 Planarity : 0.005 0.147 5119 Dihedral : 13.101 87.816 4818 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.40 % Favored : 92.35 % Rotamer Outliers : 5.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.75 (0.14), residues: 3515 helix: 1.83 (0.18), residues: 952 sheet: -0.27 (0.22), residues: 623 loop : -1.88 (0.13), residues: 1940 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7030 Ramachandran restraints generated. 3515 Oldfield, 0 Emsley, 3515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 165 time to evaluate : 3.509 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 outliers start: 164 outliers final: 148 residues processed: 328 average time/residue: 1.2021 time to fit residues: 478.6797 Evaluate side-chains 307 residues out of total 2989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 159 time to evaluate : 3.558 Switching outliers to nearest non-outliers outliers start: 148 outliers final: 148 residues processed: 2 average time/residue: 1.2494 time to fit residues: 7.7666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 292 optimal weight: 40.0000 chunk 36 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 250 optimal weight: 20.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** Z 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.104517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.059987 restraints weight = 65718.155| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.17 r_work: 0.2656 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 30173 Z= 0.324 Angle : 0.634 12.885 41275 Z= 0.326 Chirality : 0.044 0.302 4712 Planarity : 0.005 0.141 5119 Dihedral : 13.174 87.421 4818 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.88 % Favored : 91.86 % Rotamer Outliers : 5.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.82 (0.14), residues: 3515 helix: 1.72 (0.18), residues: 956 sheet: -0.27 (0.22), residues: 618 loop : -1.92 (0.13), residues: 1941 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9727.72 seconds wall clock time: 173 minutes 21.82 seconds (10401.82 seconds total)