Starting phenix.real_space_refine on Fri Jul 3 00:43:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jcy_36169/07_2026/8jcy_36169.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcy_36169/07_2026/8jcy_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_36169/07_2026/8jcy_36169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcy_36169/07_2026/8jcy_36169.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcy_36169/07_2026/8jcy_36169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcy_36169/07_2026/8jcy_36169.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8jcy_36169/07_2026/8jcy_36169.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jcy_36169/07_2026/8jcy_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-dev-6108/lib/python3.11/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 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 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: 3.66, per 1000 atoms: 0.34 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: 1.01 Conformation dependent library (CDL) restraints added in 858.4 milliseconds 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: 0.29 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: 1.84 Time building geometry restraints manager: 1.36 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 - 17.75: 6131 17.75 - 35.49: 315 35.49 - 53.24: 54 53.24 - 70.99: 9 70.99 - 88.73: 8 Dihedral angle restraints: 6517 sinusoidal: 2093 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 6514 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: 3.820 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.160 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 : 11.202 88.734 3599 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 are 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/Z covalent geometry : bond 0.00289 / 0.14 (11118) covalent geometry : angle 0.53265 / 0.25 (15261) SS BOND : bond 0.00191 / 0.08 ( 18) SS BOND : angle 0.63531 / 0.42 ( 36) hydrogen bonds : bond 0.13689 / 10.01 ( 567) hydrogen bonds : angle 5.23376 / 3.92 ( 1669) link_NAG-ASN : bond 0.00260 / 0.13 ( 2) link_NAG-ASN : angle 0.73638 / 0.33 ( 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 : 0.347 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: 0.4276 time to fit residues: 64.6799 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 : 0.437 ------------------------------------------------------------------------------- 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... 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 = 0.4463 r_free = 0.4463 target = 0.227718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.175716 restraints weight = 28210.168| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 3.75 r_work: 0.3162 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11138 Z= 0.151 Angle : 0.560 13.875 15303 Z= 0.278 Chirality : 0.042 0.289 1805 Planarity : 0.004 0.049 1965 Dihedral : 4.622 58.229 1693 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.20 % Allowed : 8.72 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1516 helix: 2.40 (0.20), residues: 705 sheet: -0.83 (0.44), residues: 161 loop : -1.57 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 347 TYR 0.025 0.001 TYR 3 104 PHE 0.024 0.002 PHE 2 589 TRP 0.009 0.001 TRP 3 297 HIS 0.003 0.001 HIS 2 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (11118) covalent geometry : angle 0.55979 / 0.28 (15261) SS BOND : bond 0.00208 / 0.10 ( 18) SS BOND : angle 0.68350 / 0.46 ( 36) hydrogen bonds : bond 0.03631 / 2.43 ( 567) hydrogen bonds : angle 4.13237 / 3.01 ( 1669) link_NAG-ASN : bond 0.00292 / 0.15 ( 2) link_NAG-ASN : angle 0.91694 / 0.41 ( 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 130 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.260 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7858 (m100) cc_final: 0.7384 (m100) REVERT: 2 520 TRP cc_start: 0.6038 (m100) cc_final: 0.5572 (m100) outliers start: 11 outliers final: 7 residues processed: 123 average time/residue: 0.3468 time to fit residues: 48.1592 Evaluate side-chains 110 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 0.1980 chunk 10 optimal weight: 0.2980 chunk 55 optimal weight: 30.0000 chunk 150 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 439 ASN ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.224844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.173084 restraints weight = 30901.379| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.78 r_work: 0.3094 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11138 Z= 0.171 Angle : 0.545 9.061 15303 Z= 0.276 Chirality : 0.042 0.201 1805 Planarity : 0.004 0.045 1965 Dihedral : 4.699 54.323 1693 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.96 % Allowed : 10.91 % Favored : 87.13 % 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 are not related in a simple way. whole: 0.52 (0.22), residues: 1516 helix: 2.32 (0.20), residues: 709 sheet: -1.00 (0.43), residues: 157 loop : -1.65 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 3 68 TYR 0.022 0.002 TYR 3 104 PHE 0.015 0.002 PHE 2 589 TRP 0.010 0.002 TRP 3 297 HIS 0.003 0.001 HIS 2 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (11118) covalent geometry : angle 0.54399 / 0.28 (15261) SS BOND : bond 0.00275 / 0.13 ( 18) SS BOND : angle 0.91134 / 0.61 ( 36) hydrogen bonds : bond 0.03753 / 2.51 ( 567) hydrogen bonds : angle 4.00610 / 2.93 ( 1669) link_NAG-ASN : bond 0.00112 / 0.05 ( 2) link_NAG-ASN : angle 1.05644 / 0.51 ( 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 123 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.402 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7885 (m100) cc_final: 0.7404 (m100) REVERT: 2 445 ARG cc_start: 0.8247 (ptm-80) cc_final: 0.7695 (mtm-85) REVERT: 2 520 TRP cc_start: 0.6030 (m100) cc_final: 0.5771 (m-10) REVERT: 3 381 SER cc_start: 0.7582 (p) cc_final: 0.7372 (p) REVERT: 3 387 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.6882 (tm-30) REVERT: 3 391 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8844 (ptm) REVERT: 3 429 LYS cc_start: 0.8656 (tttm) cc_final: 0.8174 (ttpt) outliers start: 18 outliers final: 10 residues processed: 115 average time/residue: 0.3567 time to fit residues: 45.6425 Evaluate side-chains 108 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 304 VAL Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 3 residue 83 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 78 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 48 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 128 optimal weight: 0.0980 chunk 9 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 332 GLN ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.225556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.172801 restraints weight = 27701.307| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 3.76 r_work: 0.3116 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1807 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= 0.130 Angle : 0.514 7.921 15303 Z= 0.261 Chirality : 0.041 0.171 1805 Planarity : 0.004 0.038 1965 Dihedral : 4.603 54.810 1693 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.29 % Allowed : 11.12 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.22), residues: 1516 helix: 2.41 (0.20), residues: 707 sheet: -0.94 (0.42), residues: 161 loop : -1.57 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 156 TYR 0.019 0.001 TYR 3 104 PHE 0.012 0.001 PHE 3 333 TRP 0.008 0.001 TRP 3 355 HIS 0.002 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11118) covalent geometry : angle 0.51306 / 0.26 (15261) SS BOND : bond 0.00222 / 0.10 ( 18) SS BOND : angle 0.75914 / 0.52 ( 36) hydrogen bonds : bond 0.03306 / 2.20 ( 567) hydrogen bonds : angle 3.87603 / 2.84 ( 1669) link_NAG-ASN : bond 0.00222 / 0.11 ( 2) link_NAG-ASN : angle 0.96565 / 0.45 ( 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 127 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.382 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7861 (m100) cc_final: 0.7397 (m100) REVERT: 2 405 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7633 (mmm-85) REVERT: 2 445 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7705 (mpp-170) REVERT: 2 520 TRP cc_start: 0.5841 (m100) cc_final: 0.5491 (m-10) REVERT: 3 387 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: 3 391 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8753 (ptm) REVERT: 3 429 LYS cc_start: 0.8592 (tttm) cc_final: 0.8149 (ttpt) REVERT: 3 478 TYR cc_start: 0.8670 (m-80) cc_final: 0.8470 (m-80) outliers start: 21 outliers final: 10 residues processed: 117 average time/residue: 0.3568 time to fit residues: 46.6880 Evaluate side-chains 111 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 219 THR 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 83 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 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 391 MET 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: 8.9990 chunk 68 optimal weight: 20.0000 chunk 120 optimal weight: 0.6980 chunk 101 optimal weight: 0.2980 chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 50.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.222209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.163816 restraints weight = 25305.178| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.50 r_work: 0.3098 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11138 Z= 0.252 Angle : 0.602 8.927 15303 Z= 0.305 Chirality : 0.044 0.203 1805 Planarity : 0.004 0.037 1965 Dihedral : 4.916 55.743 1693 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.94 % Allowed : 12.54 % Favored : 84.51 % 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 are not related in a simple way. whole: 0.31 (0.22), residues: 1516 helix: 2.14 (0.20), residues: 714 sheet: -1.19 (0.40), residues: 161 loop : -1.76 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 3 68 TYR 0.023 0.002 TYR 3 186 PHE 0.016 0.002 PHE 3 333 TRP 0.013 0.002 TRP 3 297 HIS 0.004 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.25 (11118) covalent geometry : angle 0.60080 / 0.30 (15261) SS BOND : bond 0.00215 / 0.10 ( 18) SS BOND : angle 0.85179 / 0.52 ( 36) hydrogen bonds : bond 0.04149 / 2.74 ( 567) hydrogen bonds : angle 4.09552 / 2.98 ( 1669) link_NAG-ASN : bond 0.00047 / 0.02 ( 2) link_NAG-ASN : angle 0.93038 / 0.43 ( 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 131 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.428 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7951 (m100) cc_final: 0.7497 (m100) REVERT: 2 405 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7640 (mmm-85) REVERT: 2 445 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7800 (mtm-85) REVERT: 2 520 TRP cc_start: 0.6132 (m100) cc_final: 0.5770 (m-10) REVERT: 3 224 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8150 (mm-30) REVERT: 3 315 HIS cc_start: 0.7894 (m90) cc_final: 0.7504 (p90) REVERT: 3 387 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: 3 391 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8849 (ptm) REVERT: 3 429 LYS cc_start: 0.8606 (tttm) cc_final: 0.8153 (ttmt) REVERT: 3 445 ASN cc_start: 0.6802 (t0) cc_final: 0.6461 (t0) outliers start: 27 outliers final: 14 residues processed: 117 average time/residue: 0.4214 time to fit residues: 54.9536 Evaluate side-chains 116 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 458 THR Chi-restraints excluded: chain 3 residue 495 ASN 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: 0.9990 chunk 124 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 141 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.228946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.186863 restraints weight = 30713.992| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 3.49 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (10 function evaluations) r_final: 0.4109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11138 Z= 0.227 Angle : 0.600 9.739 15303 Z= 0.303 Chirality : 0.043 0.194 1805 Planarity : 0.004 0.037 1965 Dihedral : 5.036 56.183 1693 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.16 % Allowed : 13.20 % Favored : 83.64 % 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 are not related in a simple way. whole: 0.21 (0.22), residues: 1516 helix: 2.09 (0.19), residues: 713 sheet: -1.43 (0.41), residues: 158 loop : -1.78 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 347 TYR 0.022 0.002 TYR 3 186 PHE 0.016 0.002 PHE 3 333 TRP 0.011 0.002 TRP 3 297 HIS 0.005 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (11118) covalent geometry : angle 0.59875 / 0.30 (15261) SS BOND : bond 0.00219 / 0.10 ( 18) SS BOND : angle 0.83838 / 0.49 ( 36) hydrogen bonds : bond 0.04007 / 2.64 ( 567) hydrogen bonds : angle 4.05884 / 2.97 ( 1669) link_NAG-ASN : bond 0.00058 / 0.03 ( 2) link_NAG-ASN : angle 0.91253 / 0.41 ( 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 130 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.338 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7986 (m100) cc_final: 0.7590 (m100) REVERT: 2 375 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6070 (tm-30) REVERT: 2 405 ARG cc_start: 0.7661 (mtp85) cc_final: 0.7369 (mmm-85) REVERT: 3 387 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6206 (tm-30) REVERT: 3 391 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8206 (ptm) REVERT: 3 429 LYS cc_start: 0.8364 (tttm) cc_final: 0.8150 (ttmt) outliers start: 29 outliers final: 18 residues processed: 120 average time/residue: 0.3662 time to fit residues: 48.8989 Evaluate side-chains 119 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 269 PHE 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 410 THR Chi-restraints excluded: chain 3 residue 458 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 143 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 8 optimal weight: 0.0570 chunk 95 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 265 GLN 3 445 ASN 3 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.230719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.185936 restraints weight = 19453.774| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 3.25 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11138 Z= 0.134 Angle : 0.537 8.773 15303 Z= 0.272 Chirality : 0.041 0.178 1805 Planarity : 0.004 0.038 1965 Dihedral : 4.862 55.974 1693 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.51 % Allowed : 14.50 % Favored : 82.99 % 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 are not related in a simple way. whole: 0.36 (0.22), residues: 1516 helix: 2.21 (0.20), residues: 714 sheet: -1.31 (0.42), residues: 158 loop : -1.71 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 445 TYR 0.016 0.001 TYR 3 104 PHE 0.020 0.001 PHE 3 195 TRP 0.013 0.001 TRP 2 520 HIS 0.002 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (11118) covalent geometry : angle 0.53647 / 0.27 (15261) SS BOND : bond 0.00173 / 0.07 ( 18) SS BOND : angle 0.64321 / 0.41 ( 36) hydrogen bonds : bond 0.03447 / 2.29 ( 567) hydrogen bonds : angle 3.91259 / 2.87 ( 1669) link_NAG-ASN : bond 0.00105 / 0.05 ( 2) link_NAG-ASN : angle 0.92356 / 0.42 ( 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 125 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.259 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7944 (m100) cc_final: 0.7579 (m100) REVERT: 2 405 ARG cc_start: 0.7633 (mtp85) cc_final: 0.7354 (mmm-85) REVERT: 2 445 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7550 (mpp-170) REVERT: 3 387 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6173 (tm-30) REVERT: 3 391 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7976 (ptm) REVERT: 3 429 LYS cc_start: 0.8359 (tttm) cc_final: 0.8140 (ttmt) outliers start: 23 outliers final: 13 residues processed: 114 average time/residue: 0.3939 time to fit residues: 49.8834 Evaluate side-chains 112 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 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 458 THR Chi-restraints excluded: chain 3 residue 495 ASN 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: 0.6980 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.227481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.183554 restraints weight = 24640.102| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 3.33 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11138 Z= 0.243 Angle : 0.612 9.227 15303 Z= 0.310 Chirality : 0.044 0.201 1805 Planarity : 0.004 0.037 1965 Dihedral : 5.039 56.132 1693 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.94 % Allowed : 15.05 % Favored : 82.01 % 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 are not related in a simple way. whole: 0.19 (0.22), residues: 1516 helix: 2.11 (0.20), residues: 713 sheet: -1.54 (0.40), residues: 170 loop : -1.80 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 445 TYR 0.022 0.002 TYR 3 186 PHE 0.016 0.002 PHE 3 333 TRP 0.013 0.002 TRP 3 297 HIS 0.004 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.24 (11118) covalent geometry : angle 0.61121 / 0.31 (15261) SS BOND : bond 0.00191 / 0.08 ( 18) SS BOND : angle 0.84988 / 0.49 ( 36) hydrogen bonds : bond 0.04138 / 2.72 ( 567) hydrogen bonds : angle 4.05565 / 2.97 ( 1669) link_NAG-ASN : bond 0.00115 / 0.05 ( 2) link_NAG-ASN : angle 0.91035 / 0.42 ( 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 131 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.389 Fit side-chains REVERT: 2 337 TRP cc_start: 0.8016 (m100) cc_final: 0.7662 (m100) REVERT: 2 375 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.6133 (tm-30) REVERT: 2 405 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7409 (mmm-85) REVERT: 3 387 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6209 (tm-30) REVERT: 3 391 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8340 (ptm) REVERT: 3 429 LYS cc_start: 0.8394 (tttm) cc_final: 0.8121 (ttmt) outliers start: 27 outliers final: 18 residues processed: 123 average time/residue: 0.3555 time to fit residues: 48.7560 Evaluate side-chains 120 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 269 PHE 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 276 MET 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: 1.9990 chunk 42 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 469 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 = 0.4471 r_free = 0.4471 target = 0.225642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.180852 restraints weight = 24482.548| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.31 r_work: 0.3256 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 11138 Z= 0.342 Angle : 0.705 10.244 15303 Z= 0.357 Chirality : 0.047 0.265 1805 Planarity : 0.005 0.039 1965 Dihedral : 5.376 57.159 1693 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.27 % Allowed : 14.61 % Favored : 82.12 % 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 are not related in a simple way. whole: -0.15 (0.22), residues: 1516 helix: 1.86 (0.20), residues: 713 sheet: -1.78 (0.38), residues: 170 loop : -1.99 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 3 347 TYR 0.027 0.002 TYR 3 186 PHE 0.025 0.002 PHE 3 195 TRP 0.016 0.002 TRP 3 297 HIS 0.006 0.002 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00827 / 0.34 (11118) covalent geometry : angle 0.70422 / 0.36 (15261) SS BOND : bond 0.00298 / 0.15 ( 18) SS BOND : angle 0.99429 / 0.57 ( 36) hydrogen bonds : bond 0.04786 / 3.15 ( 567) hydrogen bonds : angle 4.28130 / 3.13 ( 1669) link_NAG-ASN : bond 0.00351 / 0.17 ( 2) link_NAG-ASN : angle 1.06408 / 0.52 ( 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 131 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.403 Fit side-chains REVERT: 2 337 TRP cc_start: 0.8098 (m100) cc_final: 0.7682 (m100) REVERT: 2 375 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.6628 (tm-30) REVERT: 2 405 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7907 (mmm-85) REVERT: 3 102 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8484 (m-30) REVERT: 3 387 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: 3 391 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8830 (ptm) REVERT: 3 429 LYS cc_start: 0.8728 (tttm) cc_final: 0.8387 (ttmt) REVERT: 3 445 ASN cc_start: 0.7617 (t0) cc_final: 0.7309 (p0) outliers start: 30 outliers final: 20 residues processed: 120 average time/residue: 0.3923 time to fit residues: 52.6241 Evaluate side-chains 117 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 269 PHE 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 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: 0.0570 chunk 141 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 30.0000 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.228684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.182952 restraints weight = 21688.073| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 3.47 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11138 Z= 0.147 Angle : 0.592 10.973 15303 Z= 0.299 Chirality : 0.042 0.198 1805 Planarity : 0.004 0.040 1965 Dihedral : 5.161 57.455 1693 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.07 % Allowed : 16.14 % 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 are not related in a simple way. whole: 0.10 (0.22), residues: 1516 helix: 2.05 (0.20), residues: 714 sheet: -1.67 (0.39), residues: 170 loop : -1.86 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 445 TYR 0.021 0.002 TYR 3 104 PHE 0.015 0.001 PHE 3 275 TRP 0.013 0.001 TRP 2 520 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11118) covalent geometry : angle 0.59128 / 0.30 (15261) SS BOND : bond 0.00185 / 0.08 ( 18) SS BOND : angle 0.74038 / 0.43 ( 36) hydrogen bonds : bond 0.03778 / 2.52 ( 567) hydrogen bonds : angle 4.03064 / 2.96 ( 1669) link_NAG-ASN : bond 0.00073 / 0.04 ( 2) link_NAG-ASN : angle 0.96959 / 0.47 ( 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: 19 poor density : 97 time to evaluate : 0.405 Fit side-chains REVERT: 2 337 TRP cc_start: 0.8015 (m100) cc_final: 0.7661 (m100) REVERT: 2 405 ARG cc_start: 0.7678 (mtp85) cc_final: 0.7462 (mmm-85) REVERT: 3 232 GLN cc_start: 0.8199 (mt0) cc_final: 0.7989 (mt0) REVERT: 3 387 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6197 (tm-30) REVERT: 3 391 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7746 (ptm) REVERT: 3 429 LYS cc_start: 0.8431 (tttm) cc_final: 0.8155 (ttmt) outliers start: 19 outliers final: 13 residues processed: 111 average time/residue: 0.3877 time to fit residues: 48.1054 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 : 0.355 ------------------------------------------------------------------------------- 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 269 PHE 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 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 128 optimal weight: 0.0370 chunk 86 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 265 GLN 3 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.230524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.186535 restraints weight = 16543.251| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.40 r_work: 0.3333 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11138 Z= 0.132 Angle : 0.549 10.927 15303 Z= 0.279 Chirality : 0.041 0.176 1805 Planarity : 0.004 0.038 1965 Dihedral : 4.867 55.888 1693 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.29 % Allowed : 15.70 % Favored : 82.01 % 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 are not related in a simple way. whole: 0.29 (0.22), residues: 1516 helix: 2.18 (0.20), residues: 715 sheet: -1.48 (0.40), residues: 170 loop : -1.76 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 445 TYR 0.020 0.001 TYR 3 104 PHE 0.027 0.001 PHE 3 195 TRP 0.009 0.001 TRP 3 355 HIS 0.002 0.000 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (11118) covalent geometry : angle 0.54765 / 0.28 (15261) SS BOND : bond 0.00212 / 0.10 ( 18) SS BOND : angle 0.81309 / 0.47 ( 36) hydrogen bonds : bond 0.03395 / 2.25 ( 567) hydrogen bonds : angle 3.91086 / 2.87 ( 1669) link_NAG-ASN : bond 0.00067 / 0.03 ( 2) link_NAG-ASN : angle 0.99987 / 0.48 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3185.85 seconds wall clock time: 55 minutes 1.06 seconds (3301.06 seconds total)