Starting phenix.real_space_refine on Fri Jul 3 00:13:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jcu_36165/07_2026/8jcu_36165.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcu_36165/07_2026/8jcu_36165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jcu_36165/07_2026/8jcu_36165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcu_36165/07_2026/8jcu_36165.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jcu_36165/07_2026/8jcu_36165.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jcu_36165/07_2026/8jcu_36165.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jcu_36165/07_2026/8jcu_36165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcu_36165/07_2026/8jcu_36165.cif" } resolution = 2.8 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= 0.040 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 6814 2.51 5 N 1915 2.21 5 O 2041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 10830 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5371 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 37, 'TRANS': 724} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 591 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 13, 'GLN:plan1': 6, 'ASN:plan1': 6, 'GLU:plan': 10, 'PHE:plan': 11, 'TRP:plan': 4, 'TYR:plan': 7, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 331 Chain: "3" Number of atoms: 5379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 5379 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 30, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 718 Unresolved non-hydrogen angles: 923 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 9, 'ASN:plan1': 8, 'ARG:plan': 9, 'HIS:plan': 3, 'ASP:plan': 10, 'TRP:plan': 4, 'TYR:plan': 11, 'PHE:plan': 16} Unresolved non-hydrogen planarities: 383 Chain: "2" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.17, per 1000 atoms: 0.20 Number of scatterers: 10830 At special positions: 0 Unit cell: (91.035, 121.023, 184.212, 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 2041 8.00 N 1915 7.00 C 6814 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=2.04 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.03 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 21102 " - " ASN 2 203 " " NAG 32001 " - " ASN 3 209 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 482.6 milliseconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2866 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 9 sheets defined 47.9% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain '2' and resid 58 through 74 Processing helix chain '2' and resid 94 through 102 Processing helix chain '2' and resid 104 through 110 Processing helix chain '2' and resid 144 through 157 removed outlier: 4.250A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) Processing helix chain '2' and resid 169 through 173 removed outlier: 3.874A pdb=" N SER 2 173 " --> pdb=" O ALA 2 170 " (cutoff:3.500A) Processing helix chain '2' and resid 189 through 202 removed outlier: 3.530A pdb=" N LYS 2 193 " --> pdb=" O PHE 2 189 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 230 removed outlier: 3.578A pdb=" N ALA 2 230 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 259 Processing helix chain '2' and resid 271 through 286 Processing helix chain '2' and resid 324 through 333 Processing helix chain '2' and resid 344 through 353 Processing helix chain '2' and resid 377 through 400 Processing helix chain '2' and resid 414 through 423 Processing helix chain '2' and resid 485 through 489 removed outlier: 3.994A pdb=" N SER 2 489 " --> pdb=" O PRO 2 486 " (cutoff:3.500A) Processing helix chain '2' and resid 568 through 589 Processing helix chain '2' and resid 595 through 601 Processing helix chain '2' and resid 602 through 625 removed outlier: 3.657A pdb=" N ILE 2 608 " --> pdb=" O GLU 2 604 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR 2 617 " --> pdb=" O VAL 2 613 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR 2 620 " --> pdb=" O CYS 2 616 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE 2 621 " --> pdb=" O TYR 2 617 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE 2 622 " --> pdb=" O CYS 2 618 " (cutoff:3.500A) Processing helix chain '2' and resid 630 through 659 removed outlier: 3.556A pdb=" N LEU 2 639 " --> pdb=" O ARG 2 635 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER 2 644 " --> pdb=" O GLY 2 640 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS 2 646 " --> pdb=" O ALA 2 642 " (cutoff:3.500A) Processing helix chain '2' and resid 676 through 699 removed outlier: 3.630A pdb=" N ILE 2 693 " --> pdb=" O GLY 2 689 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL 2 694 " --> pdb=" O GLN 2 690 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA 2 696 " --> pdb=" O LEU 2 692 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL 2 699 " --> pdb=" O VAL 2 695 " (cutoff:3.500A) Processing helix chain '2' and resid 725 through 749 removed outlier: 3.565A pdb=" N ASN 2 735 " --> pdb=" O SER 2 731 " (cutoff:3.500A) Processing helix chain '2' and resid 755 through 784 removed outlier: 3.747A pdb=" N LEU 2 777 " --> pdb=" O TRP 2 773 " (cutoff:3.500A) Proline residue: 2 778 - end of helix removed outlier: 3.747A pdb=" N TYR 2 781 " --> pdb=" O LEU 2 777 " (cutoff:3.500A) Processing helix chain '2' and resid 786 through 807 Processing helix chain '2' and resid 809 through 819 removed outlier: 3.778A pdb=" N LYS 2 813 " --> pdb=" O LEU 2 809 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 82 Processing helix chain '3' and resid 101 through 110 removed outlier: 3.553A pdb=" N GLU 3 107 " --> pdb=" O THR 3 103 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN 3 108 " --> pdb=" O TYR 3 104 " (cutoff:3.500A) Processing helix chain '3' and resid 111 through 117 removed outlier: 3.722A pdb=" N ARG 3 114 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA 3 115 " --> pdb=" O PHE 3 112 " (cutoff:3.500A) Processing helix chain '3' and resid 150 through 163 removed outlier: 4.078A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 175 through 180 Processing helix chain '3' and resid 195 through 208 removed outlier: 3.596A pdb=" N LYS 3 199 " --> pdb=" O PHE 3 195 " (cutoff:3.500A) Processing helix chain '3' and resid 221 through 237 removed outlier: 3.939A pdb=" N THR 3 225 " --> pdb=" O ASP 3 221 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU 3 231 " --> pdb=" O ILE 3 227 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN 3 232 " --> pdb=" O GLU 3 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU 3 233 " --> pdb=" O ALA 3 229 " (cutoff:3.500A) Processing helix chain '3' and resid 252 through 265 removed outlier: 3.500A pdb=" N TYR 3 256 " --> pdb=" O ILE 3 252 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 292 removed outlier: 3.512A pdb=" N ARG 3 282 " --> pdb=" O SER 3 278 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU 3 283 " --> pdb=" O ASP 3 279 " (cutoff:3.500A) Processing helix chain '3' and resid 330 through 339 removed outlier: 3.526A pdb=" N ASP 3 334 " --> pdb=" O VAL 3 330 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR 3 336 " --> pdb=" O GLN 3 332 " (cutoff:3.500A) Processing helix chain '3' and resid 350 through 360 Processing helix chain '3' and resid 389 through 412 Processing helix chain '3' and resid 420 through 425 removed outlier: 4.346A pdb=" N ILE 3 424 " --> pdb=" O ASP 3 420 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU 3 425 " --> pdb=" O ALA 3 421 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 420 through 425' Processing helix chain '3' and resid 426 through 433 Processing helix chain '3' and resid 434 through 438 removed outlier: 3.796A pdb=" N ILE 3 438 " --> pdb=" O LEU 3 435 " (cutoff:3.500A) Processing helix chain '3' and resid 574 through 601 removed outlier: 3.853A 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: 3.997A pdb=" N THR 3 629 " --> pdb=" O SER 3 625 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE 3 631 " --> pdb=" O CYS 3 627 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE 3 633 " --> pdb=" O THR 3 629 " (cutoff:3.500A) Processing helix chain '3' and resid 639 through 665 removed outlier: 3.804A pdb=" N LEU 3 646 " --> pdb=" O ALA 3 642 " (cutoff:3.500A) Processing helix chain '3' and resid 683 through 700 Processing helix chain '3' and resid 702 through 707 removed outlier: 3.967A pdb=" N LEU 3 707 " --> pdb=" O VAL 3 703 " (cutoff:3.500A) Processing helix chain '3' and resid 733 through 758 removed outlier: 3.632A pdb=" N VAL 3 745 " --> pdb=" O LEU 3 741 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU 3 747 " --> pdb=" O TYR 3 743 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL 3 748 " --> pdb=" O ASP 3 744 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR 3 754 " --> pdb=" O LEU 3 750 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA 3 755 " --> pdb=" O CYS 3 751 " (cutoff:3.500A) Processing helix chain '3' and resid 764 through 792 removed outlier: 3.824A pdb=" N TYR 3 776 " --> pdb=" O GLY 3 772 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR 3 777 " --> pdb=" O PHE 3 773 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU 3 786 " --> pdb=" O TRP 3 782 " (cutoff:3.500A) Proline residue: 3 787 - end of helix removed outlier: 3.853A pdb=" N VAL 3 791 " --> pdb=" O PRO 3 787 " (cutoff:3.500A) Processing helix chain '3' and resid 796 through 826 removed outlier: 4.488A 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: 3.730A pdb=" N ALA 2 86 " --> pdb=" O LEU 2 28 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL 2 33 " --> pdb=" O GLY 2 138 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE 2 140 " --> pdb=" O VAL 2 33 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY 2 35 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ILE 2 163 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 6.606A 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 239 removed outlier: 7.926A pdb=" N VAL 2 207 " --> pdb=" O ALA 2 236 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N SER 2 238 " --> pdb=" O VAL 2 207 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR 2 209 " --> pdb=" O SER 2 238 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR 2 206 " --> pdb=" O VAL 2 265 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL 2 267 " --> pdb=" O TYR 2 206 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER 2 208 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA 2 266 " --> pdb=" O VAL 2 292 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP 2 291 " --> pdb=" O ILE 2 315 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE 2 317 " --> pdb=" O TRP 2 291 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA 2 293 " --> pdb=" O ILE 2 317 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LEU 2 319 " --> pdb=" O ALA 2 293 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR 2 453 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR 2 473 " --> pdb=" O TYR 2 453 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE 2 455 " --> pdb=" O VAL 2 471 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU 2 459 " --> pdb=" O ARG 2 467 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG 2 467 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 428 through 429 removed outlier: 4.010A pdb=" N PHE 2 428 " --> pdb=" O VAL 2 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 32 through 33 removed outlier: 6.519A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL 3 40 " --> pdb=" O ILE 3 142 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY 3 144 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ILE 3 169 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL 3 145 " --> pdb=" O ILE 3 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 48 through 50 removed outlier: 4.067A pdb=" N ARG 3 59 " --> pdb=" O GLU 3 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 240 through 247 removed outlier: 7.605A pdb=" N VAL 3 213 " --> pdb=" O ALA 3 242 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA 3 244 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR 3 215 " --> pdb=" O ALA 3 244 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LYS 3 246 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA 3 217 " --> pdb=" O LYS 3 246 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR 3 212 " --> pdb=" O VAL 3 271 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL 3 273 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER 3 214 " --> pdb=" O VAL 3 273 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N TRP 3 297 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU 3 323 " --> pdb=" O TRP 3 297 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA 3 299 " --> pdb=" O LEU 3 323 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N LEU 3 325 " --> pdb=" O ALA 3 299 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR 3 466 " --> pdb=" O HIS 3 485 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N HIS 3 485 " --> pdb=" O TYR 3 466 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL 3 468 " --> pdb=" O VAL 3 483 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 361 through 362 Processing sheet with id=AA9, first strand: chain '3' and resid 440 through 441 524 hydrogen bonds defined for protein. 1542 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: 1.34 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3680 1.35 - 1.47: 2635 1.47 - 1.59: 4659 1.59 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 11050 Sorted by residual: bond pdb=" CAT Z99 21101 " pdb=" OAP Z99 21101 " ideal model delta sigma weight residual 1.364 1.456 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" CAT Z99 32002 " pdb=" OAP Z99 32002 " ideal model delta sigma weight residual 1.364 1.452 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CAS Z99 21101 " pdb=" OAP Z99 21101 " ideal model delta sigma weight residual 1.369 1.452 -0.083 2.00e-02 2.50e+03 1.70e+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 1.62e+01 bond pdb=" CAO Z99 32002 " pdb=" CAZ Z99 32002 " ideal model delta sigma weight residual 1.488 1.530 -0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 11045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 14821 1.70 - 3.39: 212 3.39 - 5.09: 43 5.09 - 6.79: 17 6.79 - 8.48: 5 Bond angle restraints: 15098 Sorted by residual: angle pdb=" N VAL 3 639 " pdb=" CA VAL 3 639 " pdb=" C VAL 3 639 " ideal model delta sigma weight residual 113.20 108.69 4.51 9.60e-01 1.09e+00 2.21e+01 angle pdb=" CA GLY 2 570 " pdb=" C GLY 2 570 " pdb=" N PRO 2 571 " ideal model delta sigma weight residual 119.27 116.63 2.64 8.50e-01 1.38e+00 9.63e+00 angle pdb=" CAX Z99 21101 " pdb=" CAZ Z99 21101 " pdb=" CAY Z99 21101 " ideal model delta sigma weight residual 120.67 112.19 8.48 3.00e+00 1.11e-01 8.00e+00 angle pdb=" N PHE 3 275 " pdb=" CA PHE 3 275 " pdb=" C PHE 3 275 " ideal model delta sigma weight residual 110.44 107.09 3.35 1.20e+00 6.94e-01 7.81e+00 angle pdb=" CA GLY 2 570 " pdb=" C GLY 2 570 " pdb=" O GLY 2 570 " ideal model delta sigma weight residual 119.65 121.51 -1.86 6.70e-01 2.23e+00 7.72e+00 ... (remaining 15093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6131 17.76 - 35.53: 363 35.53 - 53.29: 66 53.29 - 71.05: 14 71.05 - 88.81: 7 Dihedral angle restraints: 6581 sinusoidal: 2152 harmonic: 4429 Sorted by residual: dihedral pdb=" CB CYS 2 50 " pdb=" SG CYS 2 50 " pdb=" SG CYS 2 92 " pdb=" CB CYS 2 92 " ideal model delta sinusoidal sigma weight residual 93.00 9.12 83.88 1 1.00e+01 1.00e-02 8.58e+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 12.74 80.26 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CB CYS 3 412 " pdb=" SG CYS 3 412 " pdb=" SG CYS 3 419 " pdb=" CB CYS 3 419 " ideal model delta sinusoidal sigma weight residual 93.00 171.91 -78.91 1 1.00e+01 1.00e-02 7.75e+01 ... (remaining 6578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.054: 1749 1.054 - 2.108: 0 2.108 - 3.162: 0 3.162 - 4.216: 0 4.216 - 5.270: 2 Chirality restraints: 1751 Sorted by residual: 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 -2.66 5.27 2.00e-01 2.50e+01 6.94e+02 chirality pdb=" CAW Z99 21101 " pdb=" CAN Z99 21101 " pdb=" CAU Z99 21101 " pdb=" CAV Z99 21101 " both_signs ideal model delta sigma weight residual False 2.61 -2.55 5.16 2.00e-01 2.50e+01 6.65e+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 -2.75 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 1748 not shown) Planarity restraints: 1993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL 3 504 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO 3 505 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO 3 505 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 3 505 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 2 433 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO 2 434 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO 2 434 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO 2 434 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG 3 261 " 0.125 9.50e-02 1.11e+02 5.64e-02 2.51e+00 pdb=" NE ARG 3 261 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG 3 261 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG 3 261 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG 3 261 " 0.000 2.00e-02 2.50e+03 ... (remaining 1990 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2658 2.79 - 3.32: 10353 3.32 - 3.85: 17473 3.85 - 4.37: 19851 4.37 - 4.90: 34271 Nonbonded interactions: 84606 Sorted by model distance: nonbonded pdb=" O ASP 3 97 " pdb=" NE2 GLN 3 108 " model vdw 2.268 3.120 nonbonded pdb=" OD1 ASP 2 49 " pdb=" NZ LYS 2 94 " model vdw 2.301 3.120 nonbonded pdb=" OG SER 3 218 " pdb=" OD2 ASP 3 280 " model vdw 2.312 3.040 nonbonded pdb=" OG SER 2 148 " pdb=" OG SER 2 167 " model vdw 2.318 3.040 nonbonded pdb=" O SER 2 784 " pdb=" OG SER 2 784 " model vdw 2.335 3.040 ... (remaining 84601 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=0.20 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: 3.490 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.140 Find NCS groups from input model: 0.060 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:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 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 0.092 11070 Z= 0.141 Angle : 0.547 8.483 15140 Z= 0.269 Chirality : 0.181 5.270 1751 Planarity : 0.003 0.056 1991 Dihedral : 11.820 88.814 3661 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.18 (0.21), residues: 1515 helix: 1.83 (0.20), residues: 668 sheet: -0.52 (0.45), residues: 141 loop : -1.51 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG 3 261 TYR 0.009 0.001 TYR 3 104 PHE 0.021 0.001 PHE 3 195 TRP 0.019 0.001 TRP 2 487 HIS 0.003 0.000 HIS 3 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (11050) covalent geometry : angle 0.54487 / 0.27 (15098) SS BOND : bond 0.00243 / 0.13 ( 18) SS BOND : angle 1.06832 / 0.65 ( 36) hydrogen bonds : bond 0.24070 / 16.25 ( 524) hydrogen bonds : angle 6.07771 / 4.17 ( 1542) link_NAG-ASN : bond 0.00168 / 0.08 ( 2) link_NAG-ASN : angle 0.64479 / 0.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.238 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 142 average time/residue: 0.4078 time to fit residues: 63.9840 Evaluate side-chains 110 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 439 ASN 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: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0000 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 overall best weight: 0.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 41 HIS 2 42 GLN 2 439 ASN 3 357 GLN ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.218268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.138906 restraints weight = 12930.976| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.55 r_work: 0.3330 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11070 Z= 0.135 Angle : 0.564 13.961 15140 Z= 0.281 Chirality : 0.041 0.157 1751 Planarity : 0.004 0.037 1991 Dihedral : 3.952 32.664 1643 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.47 % Allowed : 8.94 % Favored : 89.59 % 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: 0.36 (0.22), residues: 1515 helix: 2.04 (0.20), residues: 698 sheet: -0.76 (0.43), residues: 144 loop : -1.55 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 235 TYR 0.013 0.001 TYR 3 256 PHE 0.023 0.001 PHE 3 195 TRP 0.014 0.001 TRP 2 520 HIS 0.004 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (11050) covalent geometry : angle 0.56141 / 0.28 (15098) SS BOND : bond 0.00271 / 0.16 ( 18) SS BOND : angle 1.12528 / 0.67 ( 36) hydrogen bonds : bond 0.04736 / 3.29 ( 524) hydrogen bonds : angle 4.23089 / 2.96 ( 1542) link_NAG-ASN : bond 0.00140 / 0.07 ( 2) link_NAG-ASN : angle 0.90594 / 0.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: 2 42 GLN cc_start: 0.8526 (mt0) cc_final: 0.8305 (mt0) REVERT: 2 258 LEU cc_start: 0.7259 (mt) cc_final: 0.6933 (mt) REVERT: 2 286 ASN cc_start: 0.8006 (t0) cc_final: 0.7761 (t0) REVERT: 2 524 PRO cc_start: 0.6339 (Cg_exo) cc_final: 0.6076 (Cg_endo) REVERT: 3 196 TYR cc_start: 0.8348 (m-10) cc_final: 0.8054 (m-10) REVERT: 3 228 GLU cc_start: 0.7603 (tm-30) cc_final: 0.6955 (tm-30) REVERT: 3 235 ARG cc_start: 0.6776 (mtm110) cc_final: 0.6563 (mtm-85) outliers start: 14 outliers final: 4 residues processed: 129 average time/residue: 0.4277 time to fit residues: 61.2971 Evaluate side-chains 111 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 3 residue 278 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 96 optimal weight: 0.0770 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.213545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128814 restraints weight = 12920.513| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.73 r_work: 0.3284 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11070 Z= 0.171 Angle : 0.568 8.112 15140 Z= 0.290 Chirality : 0.043 0.200 1751 Planarity : 0.004 0.043 1991 Dihedral : 4.043 17.311 1641 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.42 % Favored : 95.51 % Rotamer: Outliers : 2.42 % Allowed : 10.41 % Favored : 87.17 % 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: 0.34 (0.22), residues: 1515 helix: 2.10 (0.20), residues: 701 sheet: -0.99 (0.42), residues: 150 loop : -1.61 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 2 411 TYR 0.015 0.002 TYR 3 256 PHE 0.021 0.002 PHE 3 195 TRP 0.016 0.001 TRP 3 297 HIS 0.006 0.001 HIS 3 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (11050) covalent geometry : angle 0.55902 / 0.29 (15098) SS BOND : bond 0.00542 / 0.41 ( 18) SS BOND : angle 2.09529 / 1.33 ( 36) hydrogen bonds : bond 0.04286 / 2.92 ( 524) hydrogen bonds : angle 3.83022 / 2.66 ( 1542) link_NAG-ASN : bond 0.00069 / 0.03 ( 2) link_NAG-ASN : angle 1.24849 / 0.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.384 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7199 (mt) cc_final: 0.6840 (mt) REVERT: 2 286 ASN cc_start: 0.8129 (t0) cc_final: 0.7843 (t0) REVERT: 2 411 ARG cc_start: 0.7873 (mmt-90) cc_final: 0.7604 (mmt-90) REVERT: 2 438 HIS cc_start: 0.5544 (OUTLIER) cc_final: 0.5291 (m170) REVERT: 2 524 PRO cc_start: 0.6471 (Cg_exo) cc_final: 0.6235 (Cg_endo) REVERT: 3 196 TYR cc_start: 0.8432 (m-10) cc_final: 0.8124 (m-10) REVERT: 3 203 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7670 (mt-10) REVERT: 3 228 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7063 (tm-30) REVERT: 3 252 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.7004 (mm) REVERT: 3 262 GLU cc_start: 0.8030 (tp30) cc_final: 0.7595 (tp30) outliers start: 23 outliers final: 7 residues processed: 122 average time/residue: 0.4386 time to fit residues: 58.9408 Evaluate side-chains 112 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 817 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 30.0000 chunk 135 optimal weight: 9.9990 chunk 2 optimal weight: 0.0070 chunk 151 optimal weight: 30.0000 chunk 74 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 overall best weight: 2.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 101 GLN ** 3 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.208869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134634 restraints weight = 13257.851| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.91 r_work: 0.3287 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.105 11070 Z= 0.461 Angle : 0.817 10.461 15140 Z= 0.422 Chirality : 0.052 0.282 1751 Planarity : 0.006 0.075 1991 Dihedral : 5.050 29.377 1641 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.94 % Allowed : 11.15 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1515 helix: 1.53 (0.20), residues: 694 sheet: -1.80 (0.36), residues: 162 loop : -2.01 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 2 231 TYR 0.025 0.003 TYR 2 178 PHE 0.023 0.003 PHE 2 105 TRP 0.019 0.003 TRP 3 303 HIS 0.010 0.003 HIS 3 498 Details of bonding type rmsd/Z covalent geometry : bond 0.01114 / 0.46 (11050) covalent geometry : angle 0.80861 / 0.42 (15098) SS BOND : bond 0.00678 / 0.41 ( 18) SS BOND : angle 2.36596 / 1.43 ( 36) hydrogen bonds : bond 0.05558 / 3.77 ( 524) hydrogen bonds : angle 4.23625 / 2.95 ( 1542) link_NAG-ASN : bond 0.00581 / 0.28 ( 2) link_NAG-ASN : angle 2.30699 / 1.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 0.403 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7431 (mt) cc_final: 0.7136 (mt) REVERT: 2 286 ASN cc_start: 0.7870 (t0) cc_final: 0.7503 (t0) REVERT: 2 332 GLN cc_start: 0.8130 (mt0) cc_final: 0.7704 (mt0) REVERT: 2 476 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7055 (mt-10) REVERT: 2 520 TRP cc_start: 0.6062 (OUTLIER) cc_final: 0.5786 (t-100) REVERT: 2 524 PRO cc_start: 0.6629 (Cg_exo) cc_final: 0.6425 (Cg_endo) REVERT: 3 228 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7223 (tm-30) REVERT: 3 252 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6905 (mm) REVERT: 3 257 ASP cc_start: 0.7407 (t0) cc_final: 0.7197 (t70) REVERT: 3 275 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8195 (m-80) REVERT: 3 363 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6382 (mp) outliers start: 47 outliers final: 24 residues processed: 134 average time/residue: 0.4722 time to fit residues: 69.6041 Evaluate side-chains 125 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 213 GLU Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 2 residue 520 TRP Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 260 ILE Chi-restraints excluded: chain 3 residue 264 LEU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 817 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 32 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 139 optimal weight: 30.0000 chunk 87 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.215451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139684 restraints weight = 13172.088| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.09 r_work: 0.3360 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11070 Z= 0.133 Angle : 0.545 9.147 15140 Z= 0.281 Chirality : 0.041 0.145 1751 Planarity : 0.004 0.057 1991 Dihedral : 4.479 31.356 1641 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.31 % Allowed : 14.62 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.04 (0.22), residues: 1515 helix: 1.95 (0.20), residues: 691 sheet: -1.52 (0.37), residues: 162 loop : -1.87 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 352 TYR 0.018 0.001 TYR 2 473 PHE 0.020 0.001 PHE 3 195 TRP 0.013 0.001 TRP 2 487 HIS 0.009 0.001 HIS 3 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11050) covalent geometry : angle 0.54044 / 0.28 (15098) SS BOND : bond 0.00382 / 0.24 ( 18) SS BOND : angle 1.45976 / 0.91 ( 36) hydrogen bonds : bond 0.03658 / 2.48 ( 524) hydrogen bonds : angle 3.81483 / 2.66 ( 1542) link_NAG-ASN : bond 0.00122 / 0.06 ( 2) link_NAG-ASN : angle 1.42198 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.402 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7249 (mt) cc_final: 0.6916 (mt) REVERT: 2 332 GLN cc_start: 0.7862 (mt0) cc_final: 0.7440 (mt0) REVERT: 2 411 ARG cc_start: 0.8113 (mmt-90) cc_final: 0.7412 (mmt90) REVERT: 2 438 HIS cc_start: 0.5386 (OUTLIER) cc_final: 0.5124 (m170) REVERT: 2 476 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6782 (mp0) REVERT: 3 228 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7067 (tm-30) REVERT: 3 232 GLN cc_start: 0.7291 (mp10) cc_final: 0.7064 (mp10) REVERT: 3 252 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6772 (mm) REVERT: 3 275 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: 3 478 TYR cc_start: 0.8189 (m-80) cc_final: 0.6630 (m-80) outliers start: 22 outliers final: 11 residues processed: 115 average time/residue: 0.5476 time to fit residues: 68.5035 Evaluate side-chains 102 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 264 LEU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 32 optimal weight: 0.0770 chunk 47 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 58 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.214920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140072 restraints weight = 13275.790| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.49 r_work: 0.3304 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11070 Z= 0.155 Angle : 0.545 8.605 15140 Z= 0.279 Chirality : 0.042 0.144 1751 Planarity : 0.004 0.050 1991 Dihedral : 4.358 32.010 1641 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.84 % Allowed : 14.83 % Favored : 82.33 % 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: 0.09 (0.22), residues: 1515 helix: 2.06 (0.20), residues: 694 sheet: -1.44 (0.37), residues: 162 loop : -1.83 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 331 TYR 0.017 0.001 TYR 3 256 PHE 0.021 0.002 PHE 3 195 TRP 0.012 0.001 TRP 2 487 HIS 0.010 0.001 HIS 3 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (11050) covalent geometry : angle 0.54197 / 0.28 (15098) SS BOND : bond 0.00254 / 0.15 ( 18) SS BOND : angle 1.21140 / 0.76 ( 36) hydrogen bonds : bond 0.03594 / 2.43 ( 524) hydrogen bonds : angle 3.66364 / 2.56 ( 1542) link_NAG-ASN : bond 0.00060 / 0.03 ( 2) link_NAG-ASN : angle 1.45256 / 0.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.416 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7467 (mt) cc_final: 0.7132 (mt) REVERT: 2 332 GLN cc_start: 0.7938 (mt0) cc_final: 0.7580 (mt0) REVERT: 2 411 ARG cc_start: 0.8150 (mmt-90) cc_final: 0.7305 (mmt180) REVERT: 2 438 HIS cc_start: 0.5485 (OUTLIER) cc_final: 0.5248 (m170) REVERT: 2 476 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6941 (mp0) REVERT: 3 252 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6890 (mm) REVERT: 3 262 GLU cc_start: 0.7963 (tp30) cc_final: 0.7619 (tp30) REVERT: 3 275 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: 3 363 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6338 (mp) REVERT: 3 478 TYR cc_start: 0.7989 (m-80) cc_final: 0.6782 (m-80) outliers start: 27 outliers final: 16 residues processed: 113 average time/residue: 0.5161 time to fit residues: 63.6574 Evaluate side-chains 110 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 438 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 17 optimal weight: 1.9990 chunk 124 optimal weight: 0.0370 chunk 140 optimal weight: 0.0970 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 136 optimal weight: 30.0000 chunk 127 optimal weight: 10.0000 chunk 65 optimal weight: 0.0970 chunk 45 optimal weight: 6.9990 chunk 70 optimal weight: 40.0000 chunk 55 optimal weight: 30.0000 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 265 GLN ** 3 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.216011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141549 restraints weight = 13208.674| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.37 r_work: 0.3325 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11070 Z= 0.126 Angle : 0.523 8.429 15140 Z= 0.266 Chirality : 0.041 0.156 1751 Planarity : 0.004 0.040 1991 Dihedral : 4.255 34.180 1641 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.31 % Allowed : 15.04 % Favored : 82.65 % 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: 0.18 (0.22), residues: 1515 helix: 2.16 (0.20), residues: 693 sheet: -1.34 (0.39), residues: 152 loop : -1.82 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 445 TYR 0.015 0.001 TYR 3 256 PHE 0.020 0.001 PHE 3 195 TRP 0.012 0.001 TRP 2 487 HIS 0.010 0.001 HIS 3 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (11050) covalent geometry : angle 0.52053 / 0.26 (15098) SS BOND : bond 0.00256 / 0.16 ( 18) SS BOND : angle 1.11874 / 0.71 ( 36) hydrogen bonds : bond 0.03265 / 2.21 ( 524) hydrogen bonds : angle 3.57121 / 2.51 ( 1542) link_NAG-ASN : bond 0.00094 / 0.05 ( 2) link_NAG-ASN : angle 1.31737 / 0.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.503 Fit side-chains REVERT: 2 213 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8120 (tp30) REVERT: 2 258 LEU cc_start: 0.7443 (mt) cc_final: 0.7076 (mt) REVERT: 2 411 ARG cc_start: 0.8179 (mmt-90) cc_final: 0.7467 (mmt90) REVERT: 2 438 HIS cc_start: 0.5455 (OUTLIER) cc_final: 0.5153 (m170) REVERT: 2 476 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6724 (mp0) REVERT: 3 252 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6792 (mm) REVERT: 3 262 GLU cc_start: 0.7971 (tp30) cc_final: 0.7653 (tp30) REVERT: 3 478 TYR cc_start: 0.7981 (m-80) cc_final: 0.6781 (m-80) REVERT: 3 488 GLU cc_start: 0.8153 (tp30) cc_final: 0.7863 (tp30) outliers start: 22 outliers final: 14 residues processed: 114 average time/residue: 0.4928 time to fit residues: 61.7973 Evaluate side-chains 112 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 213 GLU Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 70 optimal weight: 50.0000 chunk 100 optimal weight: 0.7980 chunk 127 optimal weight: 0.0570 chunk 60 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 265 GLN ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.212725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135472 restraints weight = 13181.982| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.28 r_work: 0.3302 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 11070 Z= 0.253 Angle : 0.623 8.500 15140 Z= 0.317 Chirality : 0.045 0.203 1751 Planarity : 0.005 0.055 1991 Dihedral : 4.526 35.297 1641 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.36 % Allowed : 14.09 % Favored : 82.54 % 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: -0.02 (0.22), residues: 1515 helix: 1.98 (0.20), residues: 695 sheet: -1.56 (0.37), residues: 162 loop : -1.89 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 3 331 TYR 0.023 0.002 TYR 3 256 PHE 0.021 0.002 PHE 3 195 TRP 0.009 0.002 TRP 2 349 HIS 0.011 0.001 HIS 3 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.25 (11050) covalent geometry : angle 0.61922 / 0.32 (15098) SS BOND : bond 0.00343 / 0.21 ( 18) SS BOND : angle 1.32014 / 0.83 ( 36) hydrogen bonds : bond 0.04100 / 2.77 ( 524) hydrogen bonds : angle 3.72258 / 2.60 ( 1542) link_NAG-ASN : bond 0.00286 / 0.14 ( 2) link_NAG-ASN : angle 1.75780 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.421 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7491 (mt) cc_final: 0.7172 (mt) REVERT: 2 332 GLN cc_start: 0.7937 (mt0) cc_final: 0.7559 (mt0) REVERT: 2 411 ARG cc_start: 0.8188 (mmt-90) cc_final: 0.7487 (mmt90) REVERT: 2 438 HIS cc_start: 0.5459 (OUTLIER) cc_final: 0.5232 (m170) REVERT: 3 252 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6887 (mm) REVERT: 3 262 GLU cc_start: 0.7988 (tp30) cc_final: 0.7618 (tp30) REVERT: 3 275 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7997 (m-80) REVERT: 3 363 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6389 (mp) REVERT: 3 463 MET cc_start: 0.7233 (ptt) cc_final: 0.6813 (mmm) REVERT: 3 478 TYR cc_start: 0.8146 (m-80) cc_final: 0.6687 (m-80) REVERT: 3 488 GLU cc_start: 0.8151 (tp30) cc_final: 0.7918 (tp30) outliers start: 32 outliers final: 20 residues processed: 118 average time/residue: 0.4754 time to fit residues: 61.5528 Evaluate side-chains 119 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 509 CYS Chi-restraints excluded: chain 3 residue 532 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 85 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 37 optimal weight: 0.0370 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 265 GLN ** 3 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.215546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.142871 restraints weight = 13027.884| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.38 r_work: 0.3301 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11070 Z= 0.126 Angle : 0.540 8.772 15140 Z= 0.276 Chirality : 0.041 0.172 1751 Planarity : 0.004 0.041 1991 Dihedral : 4.339 36.922 1641 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.42 % Allowed : 15.14 % Favored : 82.44 % 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: 1515 helix: 2.12 (0.20), residues: 695 sheet: -1.41 (0.39), residues: 152 loop : -1.82 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 331 TYR 0.020 0.001 TYR 3 256 PHE 0.023 0.001 PHE 3 195 TRP 0.014 0.001 TRP 2 520 HIS 0.010 0.001 HIS 3 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (11050) covalent geometry : angle 0.53586 / 0.27 (15098) SS BOND : bond 0.00270 / 0.15 ( 18) SS BOND : angle 1.42333 / 0.85 ( 36) hydrogen bonds : bond 0.03250 / 2.19 ( 524) hydrogen bonds : angle 3.65565 / 2.56 ( 1542) link_NAG-ASN : bond 0.00097 / 0.05 ( 2) link_NAG-ASN : angle 1.34500 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.413 Fit side-chains REVERT: 2 213 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8248 (tp30) REVERT: 2 258 LEU cc_start: 0.7456 (mt) cc_final: 0.7109 (mt) REVERT: 2 332 GLN cc_start: 0.7932 (mt0) cc_final: 0.7594 (mt0) REVERT: 2 411 ARG cc_start: 0.8128 (mmt-90) cc_final: 0.7302 (mmt180) REVERT: 3 252 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6850 (mm) REVERT: 3 262 GLU cc_start: 0.8014 (tp30) cc_final: 0.7619 (tp30) REVERT: 3 275 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: 3 478 TYR cc_start: 0.8124 (m-80) cc_final: 0.6758 (m-80) REVERT: 3 488 GLU cc_start: 0.8139 (tp30) cc_final: 0.7863 (tp30) outliers start: 23 outliers final: 15 residues processed: 115 average time/residue: 0.4609 time to fit residues: 58.4227 Evaluate side-chains 110 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 213 GLU Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 278 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 509 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 72 optimal weight: 20.0000 chunk 57 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 265 GLN ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.214214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.137297 restraints weight = 13207.896| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.35 r_work: 0.3318 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11070 Z= 0.183 Angle : 0.577 9.356 15140 Z= 0.294 Chirality : 0.043 0.168 1751 Planarity : 0.004 0.041 1991 Dihedral : 4.386 36.428 1641 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.52 % Allowed : 15.04 % Favored : 82.44 % 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: 0.11 (0.22), residues: 1515 helix: 2.10 (0.20), residues: 695 sheet: -1.45 (0.38), residues: 162 loop : -1.84 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 331 TYR 0.024 0.002 TYR 3 256 PHE 0.019 0.002 PHE 2 589 TRP 0.019 0.001 TRP 2 487 HIS 0.011 0.001 HIS 3 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (11050) covalent geometry : angle 0.57308 / 0.29 (15098) SS BOND : bond 0.00282 / 0.17 ( 18) SS BOND : angle 1.34210 / 0.76 ( 36) hydrogen bonds : bond 0.03621 / 2.45 ( 524) hydrogen bonds : angle 3.66798 / 2.57 ( 1542) link_NAG-ASN : bond 0.00138 / 0.07 ( 2) link_NAG-ASN : angle 1.58423 / 0.91 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: 2 258 LEU cc_start: 0.7444 (mt) cc_final: 0.7110 (mt) REVERT: 2 332 GLN cc_start: 0.7887 (mt0) cc_final: 0.7558 (mt0) REVERT: 2 411 ARG cc_start: 0.8182 (mmt-90) cc_final: 0.7346 (mmt180) REVERT: 3 252 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6870 (mm) REVERT: 3 262 GLU cc_start: 0.7994 (tp30) cc_final: 0.7618 (tp30) REVERT: 3 275 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: 3 363 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6408 (mp) REVERT: 3 478 TYR cc_start: 0.8143 (m-80) cc_final: 0.6775 (m-80) REVERT: 3 488 GLU cc_start: 0.8191 (tp30) cc_final: 0.7938 (tp30) outliers start: 24 outliers final: 19 residues processed: 116 average time/residue: 0.4562 time to fit residues: 58.1020 Evaluate side-chains 117 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 307 SER Chi-restraints excluded: chain 2 residue 407 CYS Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 363 LEU 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 509 CYS Chi-restraints excluded: chain 3 residue 532 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 106 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 46 optimal weight: 0.0770 chunk 70 optimal weight: 50.0000 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 265 GLN ** 3 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.212462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135192 restraints weight = 13148.499| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.08 r_work: 0.3345 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11070 Z= 0.171 Angle : 0.565 9.358 15140 Z= 0.288 Chirality : 0.042 0.154 1751 Planarity : 0.004 0.041 1991 Dihedral : 4.397 36.980 1641 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.63 % Allowed : 14.93 % Favored : 82.44 % 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: 0.13 (0.22), residues: 1515 helix: 2.11 (0.20), residues: 695 sheet: -1.47 (0.38), residues: 162 loop : -1.82 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 331 TYR 0.022 0.002 TYR 3 256 PHE 0.014 0.002 PHE 2 589 TRP 0.018 0.001 TRP 2 487 HIS 0.011 0.001 HIS 3 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (11050) covalent geometry : angle 0.56200 / 0.29 (15098) SS BOND : bond 0.00287 / 0.18 ( 18) SS BOND : angle 1.21479 / 0.74 ( 36) hydrogen bonds : bond 0.03516 / 2.37 ( 524) hydrogen bonds : angle 3.64876 / 2.56 ( 1542) link_NAG-ASN : bond 0.00123 / 0.06 ( 2) link_NAG-ASN : angle 1.58358 / 0.89 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4496.29 seconds wall clock time: 77 minutes 13.09 seconds (4633.09 seconds total)