Starting phenix.real_space_refine on Tue May 13 22:48:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcu_36165/05_2025/8jcu_36165.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcu_36165/05_2025/8jcu_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_36165/05_2025/8jcu_36165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcu_36165/05_2025/8jcu_36165.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcu_36165/05_2025/8jcu_36165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcu_36165/05_2025/8jcu_36165.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 11, 'GLU:plan': 10, 'ARG:plan': 13} 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, 'ARG:plan': 9, 'TYR:plan': 11, 'ASN:plan1': 8, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 16, 'GLU:plan': 9, 'ASP:plan': 10} 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.08, per 1000 atoms: 0.65 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: 2.88 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.43 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: 3.37 Time building geometry restraints manager: 3.36 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 - 35.94: 6554 35.94 - 71.89: 92 71.89 - 107.83: 13 107.83 - 143.78: 4 143.78 - 179.72: 2 Dihedral angle restraints: 6665 sinusoidal: 2236 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 6662 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: 1.930 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.200 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 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 : 14.086 179.723 3745 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), 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 TRP 0.019 0.001 TRP 2 487 HIS 0.003 0.000 HIS 3 498 PHE 0.021 0.001 PHE 3 195 TYR 0.009 0.001 TYR 3 104 ARG 0.013 0.000 ARG 3 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 2) link_NAG-ASN : angle 0.64479 ( 6) hydrogen bonds : bond 0.24070 ( 524) hydrogen bonds : angle 6.07771 ( 1542) SS BOND : bond 0.00243 ( 18) SS BOND : angle 1.06832 ( 36) covalent geometry : bond 0.00281 (11050) covalent geometry : angle 0.54487 (15098) *********************** 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 : 1.185 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 142 average time/residue: 0.9258 time to fit residues: 145.7023 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 : 1.190 ------------------------------------------------------------------------------- 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 128 optimal weight: 30.0000 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4500 r_free = 0.4500 target = 0.215208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.133202 restraints weight = 12809.065| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.82 r_work: 0.3310 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 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 = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11070 Z= 0.186 Angle : 0.595 10.864 15140 Z= 0.301 Chirality : 0.043 0.194 1751 Planarity : 0.004 0.037 1991 Dihedral : 4.680 46.737 1727 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.68 % Allowed : 9.46 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1515 helix: 1.91 (0.20), residues: 698 sheet: -1.03 (0.40), residues: 156 loop : -1.58 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 3 297 HIS 0.006 0.001 HIS 2 390 PHE 0.024 0.002 PHE 3 195 TYR 0.015 0.002 TYR 2 473 ARG 0.010 0.001 ARG 3 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 2) link_NAG-ASN : angle 1.00263 ( 6) hydrogen bonds : bond 0.04873 ( 524) hydrogen bonds : angle 4.25582 ( 1542) SS BOND : bond 0.00337 ( 18) SS BOND : angle 1.26196 ( 36) covalent geometry : bond 0.00422 (11050) covalent geometry : angle 0.59218 (15098) *********************** 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 139 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 258 LEU cc_start: 0.7257 (mt) cc_final: 0.6958 (mt) REVERT: 2 286 ASN cc_start: 0.8050 (t0) cc_final: 0.7786 (t0) REVERT: 2 524 PRO cc_start: 0.6321 (Cg_exo) cc_final: 0.6058 (Cg_endo) REVERT: 3 196 TYR cc_start: 0.8360 (m-10) cc_final: 0.8064 (m-10) REVERT: 3 228 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6910 (tm-30) REVERT: 3 232 GLN cc_start: 0.7129 (mp10) cc_final: 0.6895 (mp10) outliers start: 16 outliers final: 3 residues processed: 131 average time/residue: 0.9499 time to fit residues: 137.3506 Evaluate side-chains 108 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 61 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 139 optimal weight: 30.0000 chunk 70 optimal weight: 50.0000 chunk 137 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 145 optimal weight: 50.0000 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 133 optimal weight: 20.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 101 GLN 3 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.211821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.136495 restraints weight = 13219.501| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.08 r_work: 0.3299 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- 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: 2 | |-----------------------------------------------------------------------------| |-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: 3 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.105 11070 Z= 0.418 Angle : 0.783 9.837 15140 Z= 0.401 Chirality : 0.051 0.258 1751 Planarity : 0.006 0.053 1991 Dihedral : 6.145 49.354 1725 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.89 % Allowed : 10.20 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1515 helix: 1.54 (0.20), residues: 696 sheet: -1.56 (0.37), residues: 162 loop : -1.88 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP 3 297 HIS 0.007 0.002 HIS 2 97 PHE 0.021 0.003 PHE 2 189 TYR 0.025 0.003 TYR 2 178 ARG 0.006 0.001 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 2) link_NAG-ASN : angle 2.12794 ( 6) hydrogen bonds : bond 0.05654 ( 524) hydrogen bonds : angle 4.25956 ( 1542) SS BOND : bond 0.00675 ( 18) SS BOND : angle 2.61282 ( 36) covalent geometry : bond 0.01015 (11050) covalent geometry : angle 0.77226 (15098) *********************** 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 142 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.265 Fit side-chains REVERT: 2 286 ASN cc_start: 0.7836 (t0) cc_final: 0.7548 (t0) REVERT: 2 332 GLN cc_start: 0.7994 (mt0) cc_final: 0.7574 (mt0) REVERT: 2 445 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.8004 (ptm-80) REVERT: 2 476 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7120 (mt-10) REVERT: 2 524 PRO cc_start: 0.6640 (Cg_exo) cc_final: 0.6418 (Cg_endo) REVERT: 3 196 TYR cc_start: 0.8566 (m-10) cc_final: 0.8298 (m-10) REVERT: 3 228 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7178 (tm-30) REVERT: 3 235 ARG cc_start: 0.7208 (mtm110) cc_final: 0.6890 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6939 (mm) outliers start: 37 outliers final: 16 residues processed: 129 average time/residue: 0.9951 time to fit residues: 141.3774 Evaluate side-chains 115 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 445 ARG Chi-restraints excluded: chain 2 residue 479 THR 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 191 VAL Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 260 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 388 SER Chi-restraints excluded: chain 3 residue 438 ILE 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 30 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 104 optimal weight: 0.0670 chunk 67 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 75 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.215858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.142443 restraints weight = 13126.106| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.39 r_work: 0.3313 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2651 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= 0.142 Angle : 0.548 6.326 15140 Z= 0.281 Chirality : 0.042 0.181 1751 Planarity : 0.004 0.047 1991 Dihedral : 5.288 41.059 1725 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.15 % Allowed : 12.51 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1515 helix: 1.93 (0.20), residues: 698 sheet: -1.52 (0.37), residues: 167 loop : -1.78 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 2 520 HIS 0.007 0.001 HIS 3 498 PHE 0.017 0.001 PHE 3 195 TYR 0.015 0.001 TYR 3 256 ARG 0.005 0.000 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 2) link_NAG-ASN : angle 1.24857 ( 6) hydrogen bonds : bond 0.03807 ( 524) hydrogen bonds : angle 3.86212 ( 1542) SS BOND : bond 0.00381 ( 18) SS BOND : angle 1.71769 ( 36) covalent geometry : bond 0.00318 (11050) covalent geometry : angle 0.54193 (15098) *********************** 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 132 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 1.118 Fit side-chains REVERT: 2 332 GLN cc_start: 0.7982 (mt0) cc_final: 0.7625 (mt0) REVERT: 2 411 ARG cc_start: 0.8062 (mmt-90) cc_final: 0.7384 (mmt90) REVERT: 2 438 HIS cc_start: 0.5361 (OUTLIER) cc_final: 0.5073 (m170) REVERT: 2 476 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7039 (mp0) REVERT: 2 524 PRO cc_start: 0.6691 (Cg_exo) cc_final: 0.6474 (Cg_endo) REVERT: 3 196 TYR cc_start: 0.8606 (m-10) cc_final: 0.8310 (m-10) REVERT: 3 228 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7290 (tm-30) REVERT: 3 252 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6905 (mm) REVERT: 3 262 GLU cc_start: 0.8109 (tp30) cc_final: 0.7663 (tp30) REVERT: 3 265 GLN cc_start: 0.7439 (pt0) cc_final: 0.7234 (pt0) REVERT: 3 275 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: 3 363 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6324 (mp) outliers start: 30 outliers final: 12 residues processed: 121 average time/residue: 1.0236 time to fit residues: 135.7717 Evaluate side-chains 113 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 397 ARG Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 227 ILE 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 363 LEU 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 474 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 151 optimal weight: 30.0000 chunk 30 optimal weight: 0.9990 chunk 144 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.213456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137143 restraints weight = 13108.336| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.22 r_work: 0.3297 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11070 Z= 0.241 Angle : 0.621 8.950 15140 Z= 0.316 Chirality : 0.044 0.185 1751 Planarity : 0.004 0.047 1991 Dihedral : 5.852 51.413 1725 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.26 % Allowed : 13.46 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1515 helix: 1.90 (0.20), residues: 693 sheet: -1.52 (0.37), residues: 160 loop : -1.87 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 2 520 HIS 0.009 0.001 HIS 3 498 PHE 0.016 0.002 PHE 3 74 TYR 0.019 0.002 TYR 3 256 ARG 0.008 0.000 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 2) link_NAG-ASN : angle 1.71027 ( 6) hydrogen bonds : bond 0.04249 ( 524) hydrogen bonds : angle 3.85021 ( 1542) SS BOND : bond 0.00368 ( 18) SS BOND : angle 1.66740 ( 36) covalent geometry : bond 0.00582 (11050) covalent geometry : angle 0.61522 (15098) *********************** 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 131 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 1.067 Fit side-chains REVERT: 2 286 ASN cc_start: 0.7889 (t0) cc_final: 0.7485 (t0) REVERT: 2 332 GLN cc_start: 0.7971 (mt0) cc_final: 0.7571 (mt0) REVERT: 2 411 ARG cc_start: 0.8130 (mmt-90) cc_final: 0.7300 (mmt180) REVERT: 2 438 HIS cc_start: 0.5518 (OUTLIER) cc_final: 0.5273 (m170) REVERT: 2 524 PRO cc_start: 0.6814 (Cg_exo) cc_final: 0.6613 (Cg_endo) REVERT: 3 196 TYR cc_start: 0.8584 (m-10) cc_final: 0.8307 (m-10) REVERT: 3 228 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7198 (tm-30) REVERT: 3 232 GLN cc_start: 0.7375 (mp10) cc_final: 0.7153 (mp10) REVERT: 3 235 ARG cc_start: 0.7174 (mtm110) cc_final: 0.6944 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6776 (mm) REVERT: 3 275 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: 3 363 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6351 (mp) outliers start: 31 outliers final: 22 residues processed: 121 average time/residue: 1.0365 time to fit residues: 137.5801 Evaluate side-chains 119 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 397 ARG 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 50 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 90 optimal weight: 0.0980 chunk 142 optimal weight: 30.0000 chunk 55 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 137 optimal weight: 20.0000 chunk 121 optimal weight: 0.7980 chunk 96 optimal weight: 0.0670 chunk 14 optimal weight: 0.2980 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 67 GLN 3 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.217180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.147173 restraints weight = 13275.853| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.43 r_work: 0.3413 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11070 Z= 0.105 Angle : 0.516 8.523 15140 Z= 0.262 Chirality : 0.040 0.158 1751 Planarity : 0.004 0.042 1991 Dihedral : 5.123 41.949 1725 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.10 % Allowed : 15.04 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1515 helix: 2.09 (0.20), residues: 699 sheet: -1.31 (0.39), residues: 155 loop : -1.77 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 2 487 HIS 0.007 0.001 HIS 3 498 PHE 0.015 0.001 PHE 3 195 TYR 0.014 0.001 TYR 3 256 ARG 0.008 0.000 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 2) link_NAG-ASN : angle 1.04004 ( 6) hydrogen bonds : bond 0.03107 ( 524) hydrogen bonds : angle 3.60566 ( 1542) SS BOND : bond 0.00240 ( 18) SS BOND : angle 1.27739 ( 36) covalent geometry : bond 0.00229 (11050) covalent geometry : angle 0.51280 (15098) *********************** 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: 20 poor density : 101 time to evaluate : 1.251 Fit side-chains REVERT: 2 411 ARG cc_start: 0.8033 (mmt-90) cc_final: 0.7380 (mmt90) REVERT: 2 438 HIS cc_start: 0.5292 (OUTLIER) cc_final: 0.5045 (m170) REVERT: 2 524 PRO cc_start: 0.6885 (Cg_exo) cc_final: 0.6672 (Cg_endo) REVERT: 3 196 TYR cc_start: 0.8480 (m-10) cc_final: 0.8194 (m-10) REVERT: 3 228 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7269 (tm-30) REVERT: 3 235 ARG cc_start: 0.7035 (mtm110) cc_final: 0.6830 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.6760 (mm) REVERT: 3 275 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: 3 363 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6458 (mp) REVERT: 3 391 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8725 (ppp) REVERT: 3 478 TYR cc_start: 0.8008 (m-80) cc_final: 0.6599 (m-80) REVERT: 3 488 GLU cc_start: 0.8216 (tp30) cc_final: 0.7912 (tp30) outliers start: 20 outliers final: 8 residues processed: 114 average time/residue: 0.9978 time to fit residues: 125.1878 Evaluate side-chains 106 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 397 ARG Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 3 residue 227 ILE 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 363 LEU Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 532 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 7 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 49 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 chunk 144 optimal weight: 40.0000 chunk 80 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4510 r_free = 0.4510 target = 0.216212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.143638 restraints weight = 13342.330| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.03 r_work: 0.3399 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2896 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= 0.123 Angle : 0.527 8.237 15140 Z= 0.267 Chirality : 0.041 0.148 1751 Planarity : 0.004 0.040 1991 Dihedral : 5.060 41.235 1725 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.63 % Allowed : 15.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1515 helix: 2.14 (0.20), residues: 701 sheet: -1.11 (0.41), residues: 150 loop : -1.78 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 487 HIS 0.009 0.001 HIS 3 498 PHE 0.013 0.001 PHE 3 195 TYR 0.014 0.001 TYR 3 256 ARG 0.006 0.000 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00031 ( 2) link_NAG-ASN : angle 1.25330 ( 6) hydrogen bonds : bond 0.03204 ( 524) hydrogen bonds : angle 3.54151 ( 1542) SS BOND : bond 0.00231 ( 18) SS BOND : angle 1.17741 ( 36) covalent geometry : bond 0.00281 (11050) covalent geometry : angle 0.52397 (15098) *********************** 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 122 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.150 Fit side-chains REVERT: 2 411 ARG cc_start: 0.8079 (mmt-90) cc_final: 0.7298 (mmt180) REVERT: 2 438 HIS cc_start: 0.5364 (OUTLIER) cc_final: 0.5152 (m170) REVERT: 2 524 PRO cc_start: 0.6894 (Cg_exo) cc_final: 0.6679 (Cg_endo) REVERT: 3 196 TYR cc_start: 0.8480 (m-10) cc_final: 0.8213 (m-10) REVERT: 3 235 ARG cc_start: 0.7114 (mtm110) cc_final: 0.6857 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6776 (mm) REVERT: 3 262 GLU cc_start: 0.7887 (tp30) cc_final: 0.7658 (tp30) REVERT: 3 275 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: 3 363 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6473 (mp) REVERT: 3 478 TYR cc_start: 0.8059 (m-80) cc_final: 0.6815 (m-80) REVERT: 3 488 GLU cc_start: 0.8156 (tp30) cc_final: 0.7920 (tp30) outliers start: 25 outliers final: 13 residues processed: 112 average time/residue: 0.9740 time to fit residues: 120.3436 Evaluate side-chains 111 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 397 ARG Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 76 ILE 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 264 LEU Chi-restraints excluded: chain 3 residue 275 PHE 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 532 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 50.0000 chunk 73 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 265 GLN 3 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.214804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.141096 restraints weight = 13102.268| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.99 r_work: 0.3364 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3027 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= 0.170 Angle : 0.562 8.346 15140 Z= 0.285 Chirality : 0.042 0.156 1751 Planarity : 0.004 0.040 1991 Dihedral : 5.384 46.618 1725 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.73 % Allowed : 14.51 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1515 helix: 2.11 (0.20), residues: 695 sheet: -1.23 (0.39), residues: 160 loop : -1.82 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 520 HIS 0.010 0.001 HIS 3 498 PHE 0.013 0.002 PHE 2 189 TYR 0.016 0.001 TYR 3 256 ARG 0.005 0.000 ARG 3 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 2) link_NAG-ASN : angle 1.48382 ( 6) hydrogen bonds : bond 0.03555 ( 524) hydrogen bonds : angle 3.58169 ( 1542) SS BOND : bond 0.00298 ( 18) SS BOND : angle 1.36267 ( 36) covalent geometry : bond 0.00402 (11050) covalent geometry : angle 0.55855 (15098) *********************** 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 122 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 1.184 Fit side-chains REVERT: 2 411 ARG cc_start: 0.8097 (mmt-90) cc_final: 0.7265 (mmt180) REVERT: 2 438 HIS cc_start: 0.5431 (OUTLIER) cc_final: 0.5227 (m170) REVERT: 2 589 PHE cc_start: 0.6395 (OUTLIER) cc_final: 0.6195 (p90) REVERT: 3 196 TYR cc_start: 0.8510 (m-10) cc_final: 0.8166 (m-10) REVERT: 3 235 ARG cc_start: 0.7133 (mtm110) cc_final: 0.6862 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7152 (OUTLIER) cc_final: 0.6848 (mm) REVERT: 3 262 GLU cc_start: 0.7897 (tp30) cc_final: 0.7512 (tp30) REVERT: 3 275 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: 3 363 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6462 (mp) REVERT: 3 488 GLU cc_start: 0.8082 (tp30) cc_final: 0.7841 (tp30) outliers start: 26 outliers final: 17 residues processed: 113 average time/residue: 1.0438 time to fit residues: 129.6647 Evaluate side-chains 113 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 397 ARG Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 589 PHE 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 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 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 391 MET 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 13 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 78 optimal weight: 0.0070 chunk 35 optimal weight: 0.9990 chunk 124 optimal weight: 0.0000 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 265 GLN 3 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.216123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.137960 restraints weight = 13331.779| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.93 r_work: 0.3401 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11070 Z= 0.121 Angle : 0.533 8.933 15140 Z= 0.268 Chirality : 0.041 0.152 1751 Planarity : 0.004 0.040 1991 Dihedral : 5.144 43.782 1725 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.31 % Allowed : 15.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1515 helix: 2.16 (0.20), residues: 700 sheet: -1.15 (0.41), residues: 150 loop : -1.79 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 487 HIS 0.011 0.001 HIS 3 498 PHE 0.013 0.001 PHE 3 195 TYR 0.015 0.001 TYR 3 256 ARG 0.005 0.000 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 2) link_NAG-ASN : angle 1.26026 ( 6) hydrogen bonds : bond 0.03143 ( 524) hydrogen bonds : angle 3.50853 ( 1542) SS BOND : bond 0.00217 ( 18) SS BOND : angle 1.20698 ( 36) covalent geometry : bond 0.00275 (11050) covalent geometry : angle 0.52939 (15098) *********************** 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 121 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.093 Fit side-chains REVERT: 2 411 ARG cc_start: 0.8057 (mmt-90) cc_final: 0.7162 (mmt180) REVERT: 2 438 HIS cc_start: 0.5619 (OUTLIER) cc_final: 0.5386 (m170) REVERT: 3 196 TYR cc_start: 0.8572 (m-10) cc_final: 0.8276 (m-10) REVERT: 3 235 ARG cc_start: 0.6924 (mtm110) cc_final: 0.6685 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6869 (mm) REVERT: 3 262 GLU cc_start: 0.7952 (tp30) cc_final: 0.7600 (tp30) REVERT: 3 328 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6702 (pm20) REVERT: 3 363 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6193 (mp) REVERT: 3 488 GLU cc_start: 0.8184 (tp30) cc_final: 0.7914 (tp30) outliers start: 22 outliers final: 12 residues processed: 114 average time/residue: 1.0289 time to fit residues: 129.1387 Evaluate side-chains 109 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 397 ARG Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 76 ILE 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 328 GLN 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 532 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 265 GLN 3 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.214903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.141240 restraints weight = 13218.278| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.21 r_work: 0.3303 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- 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: 3 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3125 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= 0.159 Angle : 0.562 9.363 15140 Z= 0.284 Chirality : 0.042 0.154 1751 Planarity : 0.004 0.040 1991 Dihedral : 5.357 46.905 1725 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.10 % Allowed : 15.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1515 helix: 2.11 (0.20), residues: 700 sheet: -1.24 (0.41), residues: 150 loop : -1.81 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 2 487 HIS 0.011 0.001 HIS 3 498 PHE 0.013 0.002 PHE 2 189 TYR 0.017 0.001 TYR 3 256 ARG 0.004 0.000 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 2) link_NAG-ASN : angle 1.46821 ( 6) hydrogen bonds : bond 0.03425 ( 524) hydrogen bonds : angle 3.61502 ( 1542) SS BOND : bond 0.00250 ( 18) SS BOND : angle 1.24753 ( 36) covalent geometry : bond 0.00376 (11050) covalent geometry : angle 0.55871 (15098) ********************** 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 116 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 1.223 Fit side-chains REVERT: 2 411 ARG cc_start: 0.8091 (mmt-90) cc_final: 0.7250 (mmt180) REVERT: 3 196 TYR cc_start: 0.8583 (m-10) cc_final: 0.8243 (m-10) REVERT: 3 235 ARG cc_start: 0.7065 (mtm110) cc_final: 0.6793 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6822 (mm) REVERT: 3 262 GLU cc_start: 0.7967 (tp30) cc_final: 0.7536 (tp30) REVERT: 3 265 GLN cc_start: 0.7475 (pt0) cc_final: 0.7265 (pt0) REVERT: 3 275 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: 3 363 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6408 (mp) REVERT: 3 488 GLU cc_start: 0.8165 (tp30) cc_final: 0.7930 (tp30) outliers start: 20 outliers final: 13 residues processed: 108 average time/residue: 1.0237 time to fit residues: 121.7985 Evaluate side-chains 108 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 397 ARG Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 76 ILE 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 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 532 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 445 ASN 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 = 0.214460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.140804 restraints weight = 13065.381| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.22 r_work: 0.3294 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 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 = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3231 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= 0.169 Angle : 0.571 9.502 15140 Z= 0.288 Chirality : 0.042 0.156 1751 Planarity : 0.004 0.043 1991 Dihedral : 5.513 51.052 1725 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.31 % Allowed : 15.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1515 helix: 2.10 (0.20), residues: 696 sheet: -1.28 (0.39), residues: 160 loop : -1.80 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 2 487 HIS 0.011 0.001 HIS 3 498 PHE 0.021 0.002 PHE 2 589 TYR 0.017 0.001 TYR 3 256 ARG 0.004 0.000 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 2) link_NAG-ASN : angle 1.52744 ( 6) hydrogen bonds : bond 0.03495 ( 524) hydrogen bonds : angle 3.62218 ( 1542) SS BOND : bond 0.00257 ( 18) SS BOND : angle 1.26665 ( 36) covalent geometry : bond 0.00400 (11050) covalent geometry : angle 0.56754 (15098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8750.10 seconds wall clock time: 150 minutes 45.12 seconds (9045.12 seconds total)