Starting phenix.real_space_refine on Sat Aug 23 09:38:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcy_36169/08_2025/8jcy_36169.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcy_36169/08_2025/8jcy_36169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jcy_36169/08_2025/8jcy_36169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcy_36169/08_2025/8jcy_36169.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcy_36169/08_2025/8jcy_36169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcy_36169/08_2025/8jcy_36169.cif" } resolution = 2.9 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6921 2.51 5 N 1880 2.21 5 O 2013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10874 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5258 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 37, 'TRANS': 722} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 693 Unresolved non-hydrogen angles: 891 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 6, 'ARG:plan': 17, 'ASN:plan1': 7, 'GLN:plan1': 7, 'TYR:plan': 9, 'TRP:plan': 4, 'PHE:plan': 12, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 406 Chain: "3" Number of atoms: 5340 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 765, 5330 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 30, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 763 Unresolved non-hydrogen angles: 969 Unresolved non-hydrogen dihedrals: 643 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 8, 'ASN:plan1': 10, 'ARG:plan': 13, 'HIS:plan': 3, 'ASP:plan': 9, 'TYR:plan': 12, 'TRP:plan': 2, 'PHE:plan': 15} Unresolved non-hydrogen planarities: 421 Conformer: "B" Number of residues, atoms: 765, 5330 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 30, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 763 Unresolved non-hydrogen angles: 969 Unresolved non-hydrogen dihedrals: 643 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 8, 'ASN:plan1': 10, 'ARG:plan': 13, 'HIS:plan': 3, 'ASP:plan': 9, 'TYR:plan': 12, 'TRP:plan': 2, 'PHE:plan': 15} Unresolved non-hydrogen planarities: 421 bond proxies already assigned to first conformer: 5422 Chain: "2" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 124 Unusual residues: {'CLR': 3, 'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'CLR': 4, 'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS 3 485 " occ=0.68 ... (18 atoms not shown) pdb=" NE2BHIS 3 485 " occ=0.32 Time building chain proxies: 3.41, per 1000 atoms: 0.31 Number of scatterers: 10874 At special positions: 0 Unit cell: (89.964, 122.094, 183.141, 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 60 16.00 O 2013 8.00 N 1880 7.00 C 6921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 540 " - pdb=" SG CYS 2 553 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 57 " - pdb=" SG CYS 3 99 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 240 " - pdb=" SG CYS 3 527 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 361 " - pdb=" SG CYS 3 373 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 412 " - pdb=" SG CYS 3 419 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 509 " - pdb=" SG CYS 3 528 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.04 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.04 Simple disulfide: pdb=" SG CYS 3 549 " - pdb=" SG CYS 3 562 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 641 " - pdb=" SG CYS 3 730 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG 22001 " - " ASN 2 203 " " NAG 32001 " - " ASN 3 209 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 639.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 48.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain '2' and resid 58 through 74 removed outlier: 3.641A pdb=" N LEU 2 62 " --> pdb=" O GLY 2 58 " (cutoff:3.500A) Processing helix chain '2' and resid 94 through 103 removed outlier: 3.604A pdb=" N GLU 2 100 " --> pdb=" O THR 2 96 " (cutoff:3.500A) Processing helix chain '2' and resid 104 through 110 Processing helix chain '2' and resid 144 through 157 removed outlier: 4.252A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) Processing helix chain '2' and resid 169 through 173 removed outlier: 3.576A pdb=" N LEU 2 172 " --> pdb=" O SER 2 169 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER 2 173 " --> pdb=" O ALA 2 170 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 169 through 173' Processing helix chain '2' and resid 187 through 202 removed outlier: 4.220A pdb=" N GLN 2 191 " --> pdb=" O PRO 2 187 " (cutoff:3.500A) Processing helix chain '2' and resid 214 through 230 removed outlier: 4.375A pdb=" N GLU 2 218 " --> pdb=" O GLY 2 214 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR 2 219 " --> pdb=" O ASP 2 215 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY 2 220 " --> pdb=" O TYR 2 216 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU 2 226 " --> pdb=" O GLU 2 222 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU 2 227 " --> pdb=" O ALA 2 223 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 259 Processing helix chain '2' and resid 271 through 285 Processing helix chain '2' and resid 324 through 333 removed outlier: 3.517A pdb=" N SER 2 329 " --> pdb=" O SER 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 344 through 353 Processing helix chain '2' and resid 377 through 400 Processing helix chain '2' and resid 407 through 411 Processing helix chain '2' and resid 414 through 422 removed outlier: 3.547A pdb=" N LEU 2 418 " --> pdb=" O ASN 2 414 " (cutoff:3.500A) Processing helix chain '2' and resid 485 through 489 removed outlier: 3.954A pdb=" N SER 2 489 " --> pdb=" O PRO 2 486 " (cutoff:3.500A) Processing helix chain '2' and resid 568 through 591 removed outlier: 3.869A pdb=" N VAL 2 590 " --> pdb=" O LEU 2 586 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG 2 591 " --> pdb=" O GLY 2 587 " (cutoff:3.500A) Processing helix chain '2' and resid 595 through 601 Processing helix chain '2' and resid 602 through 625 Processing helix chain '2' and resid 628 through 659 Processing helix chain '2' and resid 676 through 701 Processing helix chain '2' and resid 725 through 749 Processing helix chain '2' and resid 755 through 784 Proline residue: 2 778 - end of helix removed outlier: 4.069A pdb=" N SER 2 784 " --> pdb=" O PHE 2 780 " (cutoff:3.500A) Processing helix chain '2' and resid 786 through 808 Processing helix chain '2' and resid 809 through 819 Processing helix chain '3' and resid 66 through 82 Processing helix chain '3' and resid 101 through 115 removed outlier: 3.533A pdb=" N ALA 3 105 " --> pdb=" O ARG 3 101 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU 3 110 " --> pdb=" O LEU 3 106 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE 3 112 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 150 through 162 Processing helix chain '3' and resid 175 through 180 Processing helix chain '3' and resid 196 through 208 removed outlier: 3.661A pdb=" N ALA 3 202 " --> pdb=" O ALA 3 198 " (cutoff:3.500A) Processing helix chain '3' and resid 221 through 237 Processing helix chain '3' and resid 254 through 265 Processing helix chain '3' and resid 277 through 291 Processing helix chain '3' and resid 330 through 339 Processing helix chain '3' and resid 350 through 360 Processing helix chain '3' and resid 389 through 412 Processing helix chain '3' and resid 426 through 433 Processing helix chain '3' and resid 434 through 438 removed outlier: 3.829A pdb=" N ILE 3 438 " --> pdb=" O LEU 3 435 " (cutoff:3.500A) Processing helix chain '3' and resid 574 through 601 removed outlier: 4.368A pdb=" N GLY 3 579 " --> pdb=" O ALA 3 575 " (cutoff:3.500A) Proline residue: 3 580 - end of helix Processing helix chain '3' and resid 610 through 633 removed outlier: 3.888A pdb=" N ILE 3 633 " --> pdb=" O THR 3 629 " (cutoff:3.500A) Processing helix chain '3' and resid 640 through 665 Processing helix chain '3' and resid 683 through 706 Processing helix chain '3' and resid 707 through 709 No H-bonds generated for 'chain '3' and resid 707 through 709' Processing helix chain '3' and resid 733 through 758 removed outlier: 3.757A pdb=" N ASP 3 744 " --> pdb=" O SER 3 740 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL 3 745 " --> pdb=" O LEU 3 741 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR 3 754 " --> pdb=" O LEU 3 750 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA 3 755 " --> pdb=" O CYS 3 751 " (cutoff:3.500A) Processing helix chain '3' and resid 764 through 792 removed outlier: 3.642A pdb=" N ALA 3 768 " --> pdb=" O ASN 3 764 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR 3 777 " --> pdb=" O PHE 3 773 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 3 786 " --> pdb=" O TRP 3 782 " (cutoff:3.500A) Proline residue: 3 787 - end of helix removed outlier: 3.785A pdb=" N VAL 3 791 " --> pdb=" O PRO 3 787 " (cutoff:3.500A) Processing helix chain '3' and resid 796 through 826 removed outlier: 5.197A pdb=" N ALA 3 820 " --> pdb=" O GLY 3 816 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 26 through 28 removed outlier: 6.562A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL 2 33 " --> pdb=" O GLY 2 138 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE 2 140 " --> pdb=" O VAL 2 33 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY 2 35 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ILE 2 163 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL 2 139 " --> pdb=" O ILE 2 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 41 through 43 Processing sheet with id=AA3, first strand: chain '2' and resid 234 through 235 removed outlier: 4.016A pdb=" N GLU 2 239 " --> pdb=" O THR 2 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 234 through 235 removed outlier: 4.981A pdb=" N VAL 2 265 " --> pdb=" O TYR 2 206 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA 2 266 " --> pdb=" O VAL 2 292 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP 2 291 " --> pdb=" O ILE 2 315 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE 2 317 " --> pdb=" O TRP 2 291 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA 2 293 " --> pdb=" O ILE 2 317 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N LEU 2 319 " --> pdb=" O ALA 2 293 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR 2 453 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR 2 473 " --> pdb=" O TYR 2 453 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE 2 455 " --> pdb=" O VAL 2 471 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG 2 467 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 428 through 429 removed outlier: 3.619A pdb=" N PHE 2 428 " --> pdb=" O VAL 2 441 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 510 through 512 removed outlier: 3.566A pdb=" N VAL 2 512 " --> pdb=" O LEU 2 521 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 530 through 531 Processing sheet with id=AA8, first strand: chain '3' and resid 33 through 35 removed outlier: 6.234A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL 3 40 " --> pdb=" O ILE 3 142 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY 3 144 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ILE 3 169 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL 3 145 " --> pdb=" O ILE 3 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 48 through 50 removed outlier: 4.171A pdb=" N ARG 3 59 " --> pdb=" O GLU 3 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 240 through 247 removed outlier: 7.876A pdb=" N VAL 3 213 " --> pdb=" O ALA 3 242 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA 3 244 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR 3 215 " --> pdb=" O ALA 3 244 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS 3 246 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA 3 217 " --> pdb=" O LYS 3 246 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL 3 271 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL 3 272 " --> pdb=" O VAL 3 298 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TRP 3 297 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU 3 323 " --> pdb=" O TRP 3 297 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA 3 299 " --> pdb=" O LEU 3 323 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N LEU 3 325 " --> pdb=" O ALA 3 299 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN 3 472 " --> pdb=" O TYR 3 480 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TYR 3 480 " --> pdb=" O GLN 3 472 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER 3 491 " --> pdb=" O AHIS 3 485 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 361 through 362 Processing sheet with id=AB3, first strand: chain '3' and resid 440 through 441 removed outlier: 3.549A pdb=" N PHE 3 440 " --> pdb=" O VAL 3 454 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 518 through 519 568 hydrogen bonds defined for protein. 1669 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: 1.46 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3627 1.34 - 1.46: 2552 1.46 - 1.58: 4862 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 11118 Sorted by residual: bond pdb=" CAT Z99 32002 " pdb=" OAP Z99 32002 " ideal model delta sigma weight residual 1.364 1.453 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" CAT Z99 22002 " pdb=" OAP Z99 22002 " ideal model delta sigma weight residual 1.364 1.453 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" CAS Z99 32002 " pdb=" OAP Z99 32002 " ideal model delta sigma weight residual 1.369 1.450 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" CAS Z99 22002 " pdb=" OAP Z99 22002 " ideal model delta sigma weight residual 1.369 1.449 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" CAO Z99 22002 " pdb=" CAZ Z99 22002 " ideal model delta sigma weight residual 1.488 1.533 -0.045 2.00e-02 2.50e+03 5.09e+00 ... (remaining 11113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 15058 1.92 - 3.84: 162 3.84 - 5.75: 29 5.75 - 7.67: 7 7.67 - 9.59: 5 Bond angle restraints: 15261 Sorted by residual: angle pdb=" C VAL 3 701 " pdb=" N MET 3 702 " pdb=" CA MET 3 702 " ideal model delta sigma weight residual 121.58 115.13 6.45 1.95e+00 2.63e-01 1.09e+01 angle pdb=" CAX Z99 32002 " pdb=" CAZ Z99 32002 " pdb=" CAY Z99 32002 " ideal model delta sigma weight residual 120.67 111.08 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CAX Z99 22002 " pdb=" CAZ Z99 22002 " pdb=" CAY Z99 22002 " ideal model delta sigma weight residual 120.67 111.17 9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" CAW Z99 32002 " pdb=" CAN Z99 32002 " pdb=" CAY Z99 32002 " ideal model delta sigma weight residual 117.71 108.57 9.14 3.00e+00 1.11e-01 9.28e+00 angle pdb=" CA MET 3 702 " pdb=" CB MET 3 702 " pdb=" CG MET 3 702 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.09e+00 ... (remaining 15256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 6898 35.91 - 71.83: 75 71.83 - 107.74: 16 107.74 - 143.66: 2 143.66 - 179.57: 2 Dihedral angle restraints: 6993 sinusoidal: 2569 harmonic: 4424 Sorted by residual: dihedral pdb=" CB CYS 2 234 " pdb=" SG CYS 2 234 " pdb=" SG CYS 2 518 " pdb=" CB CYS 2 518 " ideal model delta sinusoidal sigma weight residual -86.00 -170.72 84.72 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS 3 57 " pdb=" SG CYS 3 57 " pdb=" SG CYS 3 99 " pdb=" CB CYS 3 99 " ideal model delta sinusoidal sigma weight residual 93.00 12.17 80.83 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS 2 504 " pdb=" SG CYS 2 504 " pdb=" SG CYS 2 522 " pdb=" CB CYS 2 522 " ideal model delta sinusoidal sigma weight residual 93.00 16.37 76.63 1 1.00e+01 1.00e-02 7.38e+01 ... (remaining 6990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.034: 1803 1.034 - 2.068: 0 2.068 - 3.101: 0 3.101 - 4.135: 0 4.135 - 5.169: 2 Chirality restraints: 1805 Sorted by residual: chirality pdb=" CAW Z99 22002 " pdb=" CAN Z99 22002 " pdb=" CAU Z99 22002 " pdb=" CAV Z99 22002 " both_signs ideal model delta sigma weight residual False 2.61 -2.56 5.17 2.00e-01 2.50e+01 6.68e+02 chirality pdb=" CAW Z99 32002 " pdb=" CAN Z99 32002 " pdb=" CAU Z99 32002 " pdb=" CAV Z99 32002 " both_signs ideal model delta sigma weight residual False 2.61 -2.26 4.87 2.00e-01 2.50e+01 5.93e+02 chirality pdb=" CAZ Z99 32002 " pdb=" CAO Z99 32002 " pdb=" CAX Z99 32002 " pdb=" CAY Z99 32002 " both_signs ideal model delta sigma weight residual True 2.39 -2.70 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1802 not shown) Planarity restraints: 1967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG 2 411 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.38e+00 pdb=" N PRO 2 412 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO 2 412 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO 2 412 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU 3 224 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C GLU 3 224 " 0.035 2.00e-02 2.50e+03 pdb=" O GLU 3 224 " -0.013 2.00e-02 2.50e+03 pdb=" N THR 3 225 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE 3 532 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO 3 533 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO 3 533 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO 3 533 " 0.022 5.00e-02 4.00e+02 ... (remaining 1964 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 714 2.74 - 3.28: 10778 3.28 - 3.82: 18201 3.82 - 4.36: 19846 4.36 - 4.90: 35296 Nonbonded interactions: 84835 Sorted by model distance: nonbonded pdb=" OG1 THR 2 205 " pdb=" O SER 2 498 " model vdw 2.200 3.040 nonbonded pdb=" O ASP 3 97 " pdb=" NE2 GLN 3 108 " model vdw 2.200 3.120 nonbonded pdb=" O ALA 2 746 " pdb=" OG1 THR 2 749 " model vdw 2.264 3.040 nonbonded pdb=" OG SER 3 154 " pdb=" OG SER 3 173 " model vdw 2.274 3.040 nonbonded pdb=" OG SER 3 327 " pdb=" O SER 3 388 " model vdw 2.304 3.040 ... (remaining 84830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.02 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: 4.210 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.080 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 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 : 0.003 0.089 11138 Z= 0.144 Angle : 0.533 9.588 15303 Z= 0.250 Chirality : 0.172 5.169 1805 Planarity : 0.004 0.072 1965 Dihedral : 12.993 179.571 4075 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.23), residues: 1516 helix: 2.60 (0.20), residues: 693 sheet: -0.75 (0.47), residues: 151 loop : -1.55 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 433 TYR 0.023 0.001 TYR 3 104 PHE 0.012 0.001 PHE 3 275 TRP 0.007 0.001 TRP 3 706 HIS 0.001 0.000 HIS 2 438 Details of bonding type rmsd covalent geometry : bond 0.00289 (11118) covalent geometry : angle 0.53265 (15261) SS BOND : bond 0.00191 ( 18) SS BOND : angle 0.63531 ( 36) hydrogen bonds : bond 0.13689 ( 567) hydrogen bonds : angle 5.23376 ( 1669) link_NAG-ASN : bond 0.00260 ( 2) link_NAG-ASN : angle 0.73638 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.239 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7669 (m100) cc_final: 0.7389 (m100) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3807 time to fit residues: 57.5726 Evaluate side-chains 106 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.1980 chunk 149 optimal weight: 30.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 41 HIS ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.227152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.175780 restraints weight = 28226.362| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 3.79 r_work: 0.3158 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11138 Z= 0.149 Angle : 0.549 8.161 15303 Z= 0.277 Chirality : 0.042 0.232 1805 Planarity : 0.004 0.052 1965 Dihedral : 5.055 54.482 2169 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.64 % Allowed : 8.72 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.23), residues: 1516 helix: 2.36 (0.20), residues: 706 sheet: -0.87 (0.43), residues: 161 loop : -1.57 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 235 TYR 0.025 0.002 TYR 3 104 PHE 0.024 0.002 PHE 2 589 TRP 0.010 0.001 TRP 3 297 HIS 0.003 0.001 HIS 2 41 Details of bonding type rmsd covalent geometry : bond 0.00340 (11118) covalent geometry : angle 0.54771 (15261) SS BOND : bond 0.00215 ( 18) SS BOND : angle 0.79451 ( 36) hydrogen bonds : bond 0.03618 ( 567) hydrogen bonds : angle 4.11611 ( 1669) link_NAG-ASN : bond 0.00307 ( 2) link_NAG-ASN : angle 0.83123 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.432 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7865 (m100) cc_final: 0.7402 (m100) REVERT: 2 520 TRP cc_start: 0.5986 (m100) cc_final: 0.5555 (m100) REVERT: 3 429 LYS cc_start: 0.8586 (tttp) cc_final: 0.8231 (ttpt) outliers start: 15 outliers final: 8 residues processed: 124 average time/residue: 0.3619 time to fit residues: 50.2037 Evaluate side-chains 110 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 176 SER Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 458 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 chunk 55 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 439 ASN 2 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.222560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.171900 restraints weight = 30974.026| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 3.69 r_work: 0.3062 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11138 Z= 0.259 Angle : 0.620 9.321 15303 Z= 0.314 Chirality : 0.044 0.217 1805 Planarity : 0.004 0.042 1965 Dihedral : 5.479 56.353 2169 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.62 % Allowed : 10.47 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.22), residues: 1516 helix: 2.07 (0.20), residues: 715 sheet: -1.08 (0.43), residues: 151 loop : -1.80 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 3 347 TYR 0.026 0.002 TYR 3 186 PHE 0.017 0.002 PHE 3 333 TRP 0.015 0.002 TRP 3 297 HIS 0.005 0.001 HIS 2 97 Details of bonding type rmsd covalent geometry : bond 0.00617 (11118) covalent geometry : angle 0.61911 (15261) SS BOND : bond 0.00624 ( 18) SS BOND : angle 0.91315 ( 36) hydrogen bonds : bond 0.04367 ( 567) hydrogen bonds : angle 4.18946 ( 1669) link_NAG-ASN : bond 0.00051 ( 2) link_NAG-ASN : angle 0.91747 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.333 Fit side-chains REVERT: 2 254 VAL cc_start: 0.7719 (t) cc_final: 0.7513 (t) REVERT: 2 337 TRP cc_start: 0.7952 (m100) cc_final: 0.7506 (m100) REVERT: 2 405 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7670 (mmm-85) REVERT: 2 445 ARG cc_start: 0.8354 (ptm-80) cc_final: 0.7816 (mtm-85) REVERT: 2 520 TRP cc_start: 0.6037 (m100) cc_final: 0.5809 (m-10) REVERT: 3 315 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7549 (p90) REVERT: 3 387 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: 3 391 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8903 (ptm) REVERT: 3 429 LYS cc_start: 0.8665 (tttp) cc_final: 0.8250 (ttpt) outliers start: 24 outliers final: 13 residues processed: 117 average time/residue: 0.3558 time to fit residues: 46.4131 Evaluate side-chains 113 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 176 SER Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 397 ARG Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 315 HIS Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 458 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 78 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 68 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 265 GLN 3 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.224469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.174443 restraints weight = 27384.209| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.57 r_work: 0.3080 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11138 Z= 0.170 Angle : 0.551 7.884 15303 Z= 0.279 Chirality : 0.042 0.188 1805 Planarity : 0.004 0.037 1965 Dihedral : 5.483 56.783 2169 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.40 % Allowed : 11.89 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.22), residues: 1516 helix: 2.16 (0.20), residues: 715 sheet: -1.10 (0.42), residues: 151 loop : -1.78 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 68 TYR 0.017 0.002 TYR 3 104 PHE 0.014 0.001 PHE 3 333 TRP 0.008 0.001 TRP 3 355 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00402 (11118) covalent geometry : angle 0.55031 (15261) SS BOND : bond 0.00190 ( 18) SS BOND : angle 0.84832 ( 36) hydrogen bonds : bond 0.03656 ( 567) hydrogen bonds : angle 3.98742 ( 1669) link_NAG-ASN : bond 0.00123 ( 2) link_NAG-ASN : angle 0.75612 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.258 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7973 (m100) cc_final: 0.7532 (m100) REVERT: 2 405 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7620 (mmm-85) REVERT: 2 445 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7774 (mtm-85) REVERT: 2 520 TRP cc_start: 0.5979 (m100) cc_final: 0.5602 (m100) REVERT: 3 315 HIS cc_start: 0.7950 (m90) cc_final: 0.7661 (p-80) REVERT: 3 387 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: 3 391 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8762 (ptm) REVERT: 3 429 LYS cc_start: 0.8605 (tttp) cc_final: 0.8168 (ttpt) REVERT: 3 445 ASN cc_start: 0.6637 (t0) cc_final: 0.6335 (t0) outliers start: 22 outliers final: 14 residues processed: 115 average time/residue: 0.3637 time to fit residues: 46.3328 Evaluate side-chains 114 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 176 SER Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 2 residue 397 ARG Chi-restraints excluded: chain 2 residue 445 ARG Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 458 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 120 optimal weight: 0.0980 chunk 101 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 40.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 332 GLN 3 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.229022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.186837 restraints weight = 25680.636| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 3.37 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11138 Z= 0.209 Angle : 0.583 8.118 15303 Z= 0.296 Chirality : 0.043 0.198 1805 Planarity : 0.004 0.037 1965 Dihedral : 6.026 61.136 2169 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.84 % Allowed : 12.87 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.22), residues: 1516 helix: 2.12 (0.19), residues: 713 sheet: -1.54 (0.39), residues: 170 loop : -1.79 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 68 TYR 0.021 0.002 TYR 3 186 PHE 0.019 0.002 PHE 3 195 TRP 0.011 0.002 TRP 3 297 HIS 0.004 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00499 (11118) covalent geometry : angle 0.58200 (15261) SS BOND : bond 0.00197 ( 18) SS BOND : angle 0.73835 ( 36) hydrogen bonds : bond 0.04002 ( 567) hydrogen bonds : angle 4.02053 ( 1669) link_NAG-ASN : bond 0.00036 ( 2) link_NAG-ASN : angle 0.83422 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.385 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7967 (m100) cc_final: 0.7601 (m100) REVERT: 2 375 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6254 (tm-30) REVERT: 2 405 ARG cc_start: 0.7669 (mtp85) cc_final: 0.7386 (mmm-85) REVERT: 3 387 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6217 (tm-30) REVERT: 3 391 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7852 (ptm) outliers start: 26 outliers final: 15 residues processed: 115 average time/residue: 0.3937 time to fit residues: 50.1434 Evaluate side-chains 112 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 176 SER Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 397 ARG Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 458 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 30.0000 chunk 107 optimal weight: 0.9980 chunk 124 optimal weight: 0.0030 chunk 40 optimal weight: 0.5980 chunk 145 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 141 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.230387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.189413 restraints weight = 30839.391| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 3.48 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4131 r_free = 0.4131 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4131 r_free = 0.4131 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11138 Z= 0.142 Angle : 0.536 9.654 15303 Z= 0.271 Chirality : 0.041 0.168 1805 Planarity : 0.004 0.038 1965 Dihedral : 5.816 57.239 2169 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.07 % Allowed : 14.83 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.22), residues: 1516 helix: 2.28 (0.20), residues: 708 sheet: -1.34 (0.41), residues: 158 loop : -1.74 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 445 TYR 0.017 0.001 TYR 3 104 PHE 0.013 0.001 PHE 3 333 TRP 0.014 0.001 TRP 2 520 HIS 0.002 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00334 (11118) covalent geometry : angle 0.53521 (15261) SS BOND : bond 0.00192 ( 18) SS BOND : angle 0.61306 ( 36) hydrogen bonds : bond 0.03429 ( 567) hydrogen bonds : angle 3.88957 ( 1669) link_NAG-ASN : bond 0.00107 ( 2) link_NAG-ASN : angle 0.80525 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.381 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7913 (m100) cc_final: 0.7555 (m100) REVERT: 2 375 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6177 (tm-30) REVERT: 2 405 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7374 (mmm-85) REVERT: 2 445 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7489 (mpp-170) REVERT: 3 387 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6083 (tm-30) REVERT: 3 391 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8174 (ptm) outliers start: 19 outliers final: 13 residues processed: 111 average time/residue: 0.3679 time to fit residues: 45.1753 Evaluate side-chains 109 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 397 ARG Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 458 THR Chi-restraints excluded: chain 3 residue 495 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 143 optimal weight: 20.0000 chunk 3 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 88 optimal weight: 0.0050 chunk 8 optimal weight: 0.0170 chunk 95 optimal weight: 2.9990 overall best weight: 0.3832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.231419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.185971 restraints weight = 19514.216| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 3.43 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11138 Z= 0.113 Angle : 0.519 8.288 15303 Z= 0.263 Chirality : 0.040 0.196 1805 Planarity : 0.004 0.038 1965 Dihedral : 5.601 56.752 2169 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.07 % Allowed : 15.27 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.22), residues: 1516 helix: 2.35 (0.20), residues: 710 sheet: -1.21 (0.42), residues: 158 loop : -1.67 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 445 TYR 0.019 0.001 TYR 3 104 PHE 0.020 0.001 PHE 3 195 TRP 0.012 0.001 TRP 2 520 HIS 0.003 0.000 HIS 3 315 Details of bonding type rmsd covalent geometry : bond 0.00259 (11118) covalent geometry : angle 0.51876 (15261) SS BOND : bond 0.00182 ( 18) SS BOND : angle 0.56804 ( 36) hydrogen bonds : bond 0.03171 ( 567) hydrogen bonds : angle 3.79092 ( 1669) link_NAG-ASN : bond 0.00128 ( 2) link_NAG-ASN : angle 0.82325 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.387 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7890 (m100) cc_final: 0.7565 (m100) REVERT: 2 405 ARG cc_start: 0.7657 (mtp85) cc_final: 0.7372 (mmm-85) REVERT: 2 445 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7548 (mpp-170) REVERT: 3 387 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6128 (tm-30) REVERT: 3 391 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8252 (ptm) outliers start: 19 outliers final: 10 residues processed: 108 average time/residue: 0.3802 time to fit residues: 45.6640 Evaluate side-chains 104 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 397 ARG Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 391 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 138 optimal weight: 20.0000 chunk 44 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 110 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 265 GLN ** 3 445 ASN ** 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 = 0.4503 r_free = 0.4503 target = 0.228383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.185402 restraints weight = 24732.036| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 3.38 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4090 r_free = 0.4090 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4090 r_free = 0.4090 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11138 Z= 0.247 Angle : 0.615 8.992 15303 Z= 0.312 Chirality : 0.044 0.207 1805 Planarity : 0.004 0.038 1965 Dihedral : 6.194 66.788 2169 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.73 % Allowed : 15.38 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1516 helix: 2.14 (0.20), residues: 713 sheet: -1.50 (0.40), residues: 170 loop : -1.80 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 347 TYR 0.021 0.002 TYR 3 186 PHE 0.017 0.002 PHE 3 333 TRP 0.013 0.002 TRP 3 297 HIS 0.005 0.001 HIS 2 97 Details of bonding type rmsd covalent geometry : bond 0.00594 (11118) covalent geometry : angle 0.61464 (15261) SS BOND : bond 0.00212 ( 18) SS BOND : angle 0.75295 ( 36) hydrogen bonds : bond 0.04149 ( 567) hydrogen bonds : angle 4.02459 ( 1669) link_NAG-ASN : bond 0.00099 ( 2) link_NAG-ASN : angle 0.86268 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.345 Fit side-chains REVERT: 2 337 TRP cc_start: 0.8016 (m100) cc_final: 0.7668 (m100) REVERT: 2 375 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6241 (tm-30) REVERT: 2 405 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7420 (mmm-85) REVERT: 3 387 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6235 (tm-30) REVERT: 3 391 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7920 (ptm) outliers start: 25 outliers final: 15 residues processed: 113 average time/residue: 0.3547 time to fit residues: 44.9757 Evaluate side-chains 108 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 397 ARG Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 294 SER Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 458 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 102 optimal weight: 0.3980 chunk 148 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 265 GLN ** 3 445 ASN ** 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 = 0.4463 r_free = 0.4463 target = 0.224958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.180570 restraints weight = 24468.005| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 3.39 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4035 r_free = 0.4035 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4035 r_free = 0.4035 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.101 11138 Z= 0.376 Angle : 0.726 9.811 15303 Z= 0.368 Chirality : 0.048 0.296 1805 Planarity : 0.005 0.043 1965 Dihedral : 7.068 85.394 2169 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.38 % Allowed : 14.83 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.22), residues: 1516 helix: 1.81 (0.20), residues: 713 sheet: -1.82 (0.38), residues: 170 loop : -2.04 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 3 347 TYR 0.027 0.003 TYR 3 186 PHE 0.023 0.003 PHE 2 105 TRP 0.018 0.003 TRP 3 297 HIS 0.006 0.002 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00910 (11118) covalent geometry : angle 0.72510 (15261) SS BOND : bond 0.00272 ( 18) SS BOND : angle 1.02898 ( 36) hydrogen bonds : bond 0.04997 ( 567) hydrogen bonds : angle 4.30745 ( 1669) link_NAG-ASN : bond 0.00358 ( 2) link_NAG-ASN : angle 1.10627 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.384 Fit side-chains REVERT: 2 375 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.6264 (tm-30) REVERT: 2 405 ARG cc_start: 0.7715 (mtp85) cc_final: 0.7424 (mmm-85) REVERT: 3 102 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: 3 387 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6304 (tm-30) REVERT: 3 391 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7933 (ptm) outliers start: 31 outliers final: 19 residues processed: 117 average time/residue: 0.3765 time to fit residues: 48.9977 Evaluate side-chains 116 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 50 CYS Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 397 ARG Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 265 GLN Chi-restraints excluded: chain 3 residue 294 SER Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 381 SER Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 chunk 86 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 265 GLN ** 3 445 ASN ** 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 = 0.4492 r_free = 0.4492 target = 0.228321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.183057 restraints weight = 21720.900| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 3.40 r_work: 0.3167 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11138 Z= 0.150 Angle : 0.582 11.416 15303 Z= 0.296 Chirality : 0.042 0.176 1805 Planarity : 0.004 0.038 1965 Dihedral : 6.463 72.384 2169 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.96 % Allowed : 16.68 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.22), residues: 1516 helix: 2.02 (0.20), residues: 714 sheet: -1.47 (0.40), residues: 163 loop : -1.92 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 445 TYR 0.017 0.002 TYR 3 104 PHE 0.013 0.001 PHE 3 275 TRP 0.022 0.002 TRP 3 529 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00349 (11118) covalent geometry : angle 0.58136 (15261) SS BOND : bond 0.00202 ( 18) SS BOND : angle 0.69888 ( 36) hydrogen bonds : bond 0.03692 ( 567) hydrogen bonds : angle 4.01755 ( 1669) link_NAG-ASN : bond 0.00048 ( 2) link_NAG-ASN : angle 1.03969 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.345 Fit side-chains REVERT: 2 337 TRP cc_start: 0.8238 (m100) cc_final: 0.7663 (m100) REVERT: 2 405 ARG cc_start: 0.7958 (mtp85) cc_final: 0.7616 (mmm-85) REVERT: 3 387 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: 3 391 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8771 (ptm) REVERT: 3 529 TRP cc_start: 0.6433 (OUTLIER) cc_final: 0.6166 (p90) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.4025 time to fit residues: 49.4721 Evaluate side-chains 109 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 50 CYS Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 397 ARG Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 529 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 0.0040 chunk 104 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 128 optimal weight: 0.0060 chunk 86 optimal weight: 0.9990 chunk 109 optimal weight: 0.0470 chunk 4 optimal weight: 0.5980 overall best weight: 0.2506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.232061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.190650 restraints weight = 16592.063| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 2.15 r_work: 0.3405 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11138 Z= 0.105 Angle : 0.534 11.098 15303 Z= 0.269 Chirality : 0.040 0.174 1805 Planarity : 0.004 0.040 1965 Dihedral : 5.780 56.696 2169 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.42 % Allowed : 17.23 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.22), residues: 1516 helix: 2.25 (0.20), residues: 713 sheet: -1.33 (0.41), residues: 170 loop : -1.69 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 445 TYR 0.017 0.001 TYR 3 104 PHE 0.025 0.001 PHE 3 195 TRP 0.010 0.001 TRP 3 355 HIS 0.002 0.000 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00233 (11118) covalent geometry : angle 0.53323 (15261) SS BOND : bond 0.00188 ( 18) SS BOND : angle 0.58548 ( 36) hydrogen bonds : bond 0.03066 ( 567) hydrogen bonds : angle 3.79115 ( 1669) link_NAG-ASN : bond 0.00162 ( 2) link_NAG-ASN : angle 0.98259 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.13 seconds wall clock time: 49 minutes 32.67 seconds (2972.67 seconds total)