Starting phenix.real_space_refine on Tue Jul 29 06:08:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcu_36165/07_2025/8jcu_36165.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcu_36165/07_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_36165/07_2025/8jcu_36165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcu_36165/07_2025/8jcu_36165.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcu_36165/07_2025/8jcu_36165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcu_36165/07_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-5711/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: 7.40, per 1000 atoms: 0.68 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: 2.54 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: 1.61 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: 3.69 Time building geometry restraints manager: 3.06 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: 2.920 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.550 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.120 ------------------------------------------------------------------------------- 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 : 1.112 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 142 average time/residue: 0.9470 time to fit residues: 148.8725 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 : 1.154 ------------------------------------------------------------------------------- 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 = 0.133201 restraints weight = 12809.065| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.83 r_work: 0.3311 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- 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 : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 258 LEU cc_start: 0.7255 (mt) cc_final: 0.6956 (mt) REVERT: 2 286 ASN cc_start: 0.8051 (t0) cc_final: 0.7787 (t0) REVERT: 2 524 PRO cc_start: 0.6321 (Cg_exo) cc_final: 0.6058 (Cg_endo) REVERT: 3 196 TYR cc_start: 0.8359 (m-10) cc_final: 0.8064 (m-10) REVERT: 3 228 GLU cc_start: 0.7581 (tm-30) cc_final: 0.6906 (tm-30) REVERT: 3 232 GLN cc_start: 0.7126 (mp10) cc_final: 0.6891 (mp10) outliers start: 16 outliers final: 3 residues processed: 131 average time/residue: 0.9839 time to fit residues: 142.2846 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 : 1.197 ------------------------------------------------------------------------------- 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: 0.0270 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: 8.9990 chunk 145 optimal weight: 50.0000 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 133 optimal weight: 20.0000 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.214831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139416 restraints weight = 13184.520| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.20 r_work: 0.3350 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11070 Z= 0.240 Angle : 0.634 9.175 15140 Z= 0.324 Chirality : 0.045 0.193 1751 Planarity : 0.004 0.046 1991 Dihedral : 5.090 34.621 1725 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 3.15 % Allowed : 10.52 % Favored : 86.33 % 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: 0.14 (0.22), residues: 1515 helix: 1.91 (0.20), residues: 700 sheet: -1.14 (0.39), residues: 158 loop : -1.68 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 2 520 HIS 0.006 0.001 HIS 2 390 PHE 0.021 0.002 PHE 3 195 TYR 0.018 0.002 TYR 3 256 ARG 0.007 0.001 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 2) link_NAG-ASN : angle 1.51191 ( 6) hydrogen bonds : bond 0.04792 ( 524) hydrogen bonds : angle 3.96945 ( 1542) SS BOND : bond 0.00590 ( 18) SS BOND : angle 2.22427 ( 36) covalent geometry : bond 0.00572 (11050) covalent geometry : angle 0.62498 (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 136 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 1.278 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7261 (mt) cc_final: 0.6943 (mt) REVERT: 2 286 ASN cc_start: 0.8117 (t0) cc_final: 0.7818 (t0) REVERT: 2 411 ARG cc_start: 0.8088 (mmt-90) cc_final: 0.7882 (mpt-90) REVERT: 2 524 PRO cc_start: 0.6576 (Cg_exo) cc_final: 0.6343 (Cg_endo) REVERT: 3 196 TYR cc_start: 0.8442 (m-10) cc_final: 0.8198 (m-10) REVERT: 3 228 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7069 (tm-30) REVERT: 3 232 GLN cc_start: 0.7320 (mp10) cc_final: 0.7118 (mp10) REVERT: 3 235 ARG cc_start: 0.6969 (mtm110) cc_final: 0.6696 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7032 (mm) REVERT: 3 257 ASP cc_start: 0.7050 (t0) cc_final: 0.6835 (t70) REVERT: 3 488 GLU cc_start: 0.8144 (tp30) cc_final: 0.7933 (tp30) outliers start: 30 outliers final: 13 residues processed: 125 average time/residue: 0.9565 time to fit residues: 132.2963 Evaluate side-chains 109 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 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 191 VAL Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER 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: 9.9990 chunk 104 optimal weight: 0.0770 chunk 67 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.216113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.138161 restraints weight = 13125.329| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.01 r_work: 0.3383 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11070 Z= 0.159 Angle : 0.546 6.263 15140 Z= 0.278 Chirality : 0.042 0.169 1751 Planarity : 0.004 0.040 1991 Dihedral : 4.905 32.581 1725 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.36 % Allowed : 11.67 % Favored : 84.96 % 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: 2.02 (0.20), residues: 700 sheet: -1.17 (0.39), residues: 158 loop : -1.70 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 2 520 HIS 0.006 0.001 HIS 3 498 PHE 0.018 0.002 PHE 3 195 TYR 0.020 0.001 TYR 2 473 ARG 0.004 0.000 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 2) link_NAG-ASN : angle 1.24985 ( 6) hydrogen bonds : bond 0.03739 ( 524) hydrogen bonds : angle 3.77736 ( 1542) SS BOND : bond 0.00330 ( 18) SS BOND : angle 1.56939 ( 36) covalent geometry : bond 0.00369 (11050) covalent geometry : angle 0.54123 (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 135 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.038 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7438 (mt) cc_final: 0.7096 (mt) REVERT: 2 411 ARG cc_start: 0.8075 (mmt-90) cc_final: 0.7407 (mmt90) REVERT: 2 438 HIS cc_start: 0.5684 (OUTLIER) cc_final: 0.5446 (m170) REVERT: 2 524 PRO cc_start: 0.6616 (Cg_exo) cc_final: 0.6395 (Cg_endo) REVERT: 3 196 TYR cc_start: 0.8626 (m-10) cc_final: 0.8358 (m-10) REVERT: 3 228 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7397 (tm-30) REVERT: 3 235 ARG cc_start: 0.7052 (mtm110) cc_final: 0.6784 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.6966 (mm) REVERT: 3 257 ASP cc_start: 0.7083 (t0) cc_final: 0.6876 (t70) REVERT: 3 488 GLU cc_start: 0.8170 (tp30) cc_final: 0.7822 (tp30) outliers start: 32 outliers final: 18 residues processed: 122 average time/residue: 1.0225 time to fit residues: 137.8446 Evaluate side-chains 115 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 482 THR 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 109 SER Chi-restraints excluded: chain 3 residue 141 LEU 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 278 SER Chi-restraints excluded: chain 3 residue 346 HIS 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: 0.8980 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 144 optimal weight: 30.0000 chunk 41 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 101 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 = 0.4502 r_free = 0.4502 target = 0.215337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.139933 restraints weight = 13104.326| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.24 r_work: 0.3336 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11070 Z= 0.178 Angle : 0.564 8.313 15140 Z= 0.287 Chirality : 0.042 0.170 1751 Planarity : 0.004 0.040 1991 Dihedral : 5.204 40.933 1725 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.58 % Allowed : 12.83 % Favored : 83.60 % 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: 2.05 (0.20), residues: 701 sheet: -1.24 (0.38), residues: 160 loop : -1.74 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 520 HIS 0.008 0.001 HIS 3 498 PHE 0.016 0.002 PHE 3 195 TYR 0.016 0.002 TYR 3 256 ARG 0.004 0.000 ARG 2 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 2) link_NAG-ASN : angle 1.42571 ( 6) hydrogen bonds : bond 0.03804 ( 524) hydrogen bonds : angle 3.70990 ( 1542) SS BOND : bond 0.00328 ( 18) SS BOND : angle 1.40059 ( 36) covalent geometry : bond 0.00421 (11050) covalent geometry : angle 0.55966 (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: 34 poor density : 97 time to evaluate : 1.106 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7431 (mt) cc_final: 0.7098 (mt) REVERT: 2 286 ASN cc_start: 0.8052 (t0) cc_final: 0.7680 (t0) REVERT: 2 411 ARG cc_start: 0.8075 (mmt-90) cc_final: 0.7375 (mmt90) REVERT: 2 438 HIS cc_start: 0.5425 (OUTLIER) cc_final: 0.5169 (m170) REVERT: 2 524 PRO cc_start: 0.6702 (Cg_exo) cc_final: 0.6485 (Cg_endo) REVERT: 3 228 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7215 (tm-30) REVERT: 3 232 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: 3 235 ARG cc_start: 0.7038 (mtm110) cc_final: 0.6786 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6907 (mm) REVERT: 3 257 ASP cc_start: 0.7199 (t0) cc_final: 0.6997 (t70) REVERT: 3 275 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: 3 363 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6375 (mp) outliers start: 34 outliers final: 23 residues processed: 117 average time/residue: 1.0807 time to fit residues: 138.9287 Evaluate side-chains 123 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 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 109 SER 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 232 GLN 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 276 MET Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 438 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 50 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 0.0020 chunk 142 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 14 optimal weight: 0.0070 overall best weight: 0.5206 ------------------------------------------------------------------------------- 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 = 0.4513 r_free = 0.4513 target = 0.216637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140549 restraints weight = 13244.138| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.39 r_work: 0.3375 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11070 Z= 0.124 Angle : 0.525 9.247 15140 Z= 0.265 Chirality : 0.041 0.159 1751 Planarity : 0.004 0.039 1991 Dihedral : 4.970 38.166 1725 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.05 % Allowed : 14.30 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.30 (0.22), residues: 1515 helix: 2.15 (0.20), residues: 700 sheet: -1.19 (0.40), residues: 150 loop : -1.70 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 520 HIS 0.009 0.001 HIS 3 498 PHE 0.015 0.001 PHE 3 195 TYR 0.014 0.001 TYR 3 256 ARG 0.003 0.000 ARG 2 352 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 2) link_NAG-ASN : angle 1.22481 ( 6) hydrogen bonds : bond 0.03320 ( 524) hydrogen bonds : angle 3.60029 ( 1542) SS BOND : bond 0.00252 ( 18) SS BOND : angle 1.20957 ( 36) covalent geometry : bond 0.00281 (11050) covalent geometry : angle 0.52169 (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 130 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 1.278 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7323 (mt) cc_final: 0.6955 (mt) REVERT: 2 411 ARG cc_start: 0.8069 (mmt-90) cc_final: 0.7343 (mmt90) REVERT: 2 438 HIS cc_start: 0.5429 (OUTLIER) cc_final: 0.5112 (m170) REVERT: 2 524 PRO cc_start: 0.6691 (Cg_exo) cc_final: 0.6473 (Cg_endo) REVERT: 3 109 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8709 (m) REVERT: 3 228 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7220 (tm-30) REVERT: 3 235 ARG cc_start: 0.6951 (mtm110) cc_final: 0.6677 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6852 (mm) REVERT: 3 257 ASP cc_start: 0.7163 (t0) cc_final: 0.6961 (t70) REVERT: 3 275 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8040 (m-80) REVERT: 3 363 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6333 (mp) outliers start: 29 outliers final: 19 residues processed: 121 average time/residue: 1.0373 time to fit residues: 138.0874 Evaluate side-chains 119 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 76 ILE Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 141 LEU 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 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 474 VAL 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: 0.0870 chunk 64 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 141 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 144 optimal weight: 30.0000 chunk 80 optimal weight: 0.5980 overall best weight: 0.2958 ------------------------------------------------------------------------------- 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 = 0.4529 r_free = 0.4529 target = 0.218296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144474 restraints weight = 13362.330| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.19 r_work: 0.3413 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2743 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= 0.100 Angle : 0.497 8.118 15140 Z= 0.252 Chirality : 0.040 0.145 1751 Planarity : 0.003 0.039 1991 Dihedral : 4.604 31.204 1725 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.42 % Allowed : 15.25 % 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: 0.42 (0.22), residues: 1515 helix: 2.26 (0.20), residues: 701 sheet: -0.95 (0.41), residues: 150 loop : -1.70 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 2 520 HIS 0.008 0.001 HIS 3 498 PHE 0.015 0.001 PHE 3 195 TYR 0.011 0.001 TYR 3 256 ARG 0.003 0.000 ARG 3 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 2) link_NAG-ASN : angle 1.10795 ( 6) hydrogen bonds : bond 0.02888 ( 524) hydrogen bonds : angle 3.46660 ( 1542) SS BOND : bond 0.00261 ( 18) SS BOND : angle 1.02649 ( 36) covalent geometry : bond 0.00220 (11050) covalent geometry : angle 0.49484 (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 127 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.242 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7346 (mt) cc_final: 0.6979 (mt) REVERT: 2 411 ARG cc_start: 0.7995 (mmt-90) cc_final: 0.7326 (mmt90) REVERT: 2 414 ASN cc_start: 0.7245 (p0) cc_final: 0.7022 (p0) REVERT: 2 438 HIS cc_start: 0.5446 (OUTLIER) cc_final: 0.5242 (m170) REVERT: 2 476 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6715 (mp0) REVERT: 2 524 PRO cc_start: 0.6829 (Cg_exo) cc_final: 0.6597 (Cg_endo) REVERT: 2 589 PHE cc_start: 0.6587 (OUTLIER) cc_final: 0.6349 (p90) REVERT: 3 109 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8855 (t) REVERT: 3 228 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7264 (tm-30) REVERT: 3 235 ARG cc_start: 0.6889 (mtm110) cc_final: 0.6680 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6814 (mm) REVERT: 3 391 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8724 (ppp) REVERT: 3 488 GLU cc_start: 0.8188 (tp30) cc_final: 0.7776 (tp30) outliers start: 23 outliers final: 13 residues processed: 122 average time/residue: 0.9889 time to fit residues: 133.1303 Evaluate side-chains 113 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL 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 589 PHE 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 109 SER 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 379 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 20.0000 chunk 35 optimal weight: 0.0970 chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.0570 chunk 21 optimal weight: 0.1980 chunk 70 optimal weight: 30.0000 chunk 73 optimal weight: 3.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.4509 r_free = 0.4509 target = 0.216115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143416 restraints weight = 13126.114| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.12 r_work: 0.3430 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2790 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= 0.107 Angle : 0.514 8.401 15140 Z= 0.258 Chirality : 0.040 0.139 1751 Planarity : 0.003 0.046 1991 Dihedral : 4.542 32.099 1725 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.52 % Allowed : 15.25 % Favored : 82.23 % 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: 0.47 (0.22), residues: 1515 helix: 2.29 (0.20), residues: 702 sheet: -0.91 (0.42), residues: 150 loop : -1.67 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 2 520 HIS 0.010 0.001 HIS 3 498 PHE 0.015 0.001 PHE 3 195 TYR 0.013 0.001 TYR 3 256 ARG 0.008 0.000 ARG 2 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 2) link_NAG-ASN : angle 1.13272 ( 6) hydrogen bonds : bond 0.02929 ( 524) hydrogen bonds : angle 3.43605 ( 1542) SS BOND : bond 0.00206 ( 18) SS BOND : angle 1.02618 ( 36) covalent geometry : bond 0.00239 (11050) covalent geometry : angle 0.51163 (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 124 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.411 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7432 (mt) cc_final: 0.7061 (mt) REVERT: 2 411 ARG cc_start: 0.8029 (mmt-90) cc_final: 0.7205 (mmt180) REVERT: 2 414 ASN cc_start: 0.7385 (p0) cc_final: 0.7127 (p0) REVERT: 2 524 PRO cc_start: 0.6819 (Cg_exo) cc_final: 0.6594 (Cg_endo) REVERT: 2 589 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6477 (p90) REVERT: 3 228 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7366 (tm-30) REVERT: 3 235 ARG cc_start: 0.6938 (mtm110) cc_final: 0.6675 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6860 (mm) REVERT: 3 275 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8159 (m-80) REVERT: 3 363 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6396 (mp) REVERT: 3 409 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7362 (ttp-110) REVERT: 3 488 GLU cc_start: 0.8255 (tp30) cc_final: 0.7809 (tp30) outliers start: 24 outliers final: 16 residues processed: 118 average time/residue: 1.0469 time to fit residues: 136.2514 Evaluate side-chains 114 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL 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 589 PHE 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 474 VAL 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: 0.9980 chunk 94 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 124 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 149 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 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 = 0.216087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140759 restraints weight = 13329.655| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.17 r_work: 0.3371 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2932 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= 0.143 Angle : 0.550 9.043 15140 Z= 0.275 Chirality : 0.042 0.171 1751 Planarity : 0.004 0.040 1991 Dihedral : 4.826 35.054 1725 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.52 % Allowed : 15.56 % Favored : 81.91 % 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: 0.40 (0.22), residues: 1515 helix: 2.22 (0.20), residues: 702 sheet: -1.01 (0.41), residues: 150 loop : -1.68 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 2 520 HIS 0.011 0.001 HIS 3 498 PHE 0.014 0.001 PHE 3 195 TYR 0.014 0.001 TYR 3 256 ARG 0.009 0.000 ARG 2 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 2) link_NAG-ASN : angle 1.37300 ( 6) hydrogen bonds : bond 0.03280 ( 524) hydrogen bonds : angle 3.47951 ( 1542) SS BOND : bond 0.00248 ( 18) SS BOND : angle 1.08835 ( 36) covalent geometry : bond 0.00334 (11050) covalent geometry : angle 0.54708 (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 122 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: 2 258 LEU cc_start: 0.7316 (mt) cc_final: 0.6959 (mt) REVERT: 2 411 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.7162 (mmt180) REVERT: 2 414 ASN cc_start: 0.7423 (p0) cc_final: 0.7143 (p0) REVERT: 2 524 PRO cc_start: 0.6898 (Cg_exo) cc_final: 0.6683 (Cg_endo) REVERT: 2 589 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.6490 (p90) REVERT: 3 235 ARG cc_start: 0.6905 (mtm110) cc_final: 0.6651 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6758 (mm) REVERT: 3 275 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: 3 363 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6356 (mp) REVERT: 3 409 ARG cc_start: 0.7890 (mmm-85) cc_final: 0.7224 (ttp-110) REVERT: 3 488 GLU cc_start: 0.8152 (tp30) cc_final: 0.7842 (tp30) outliers start: 24 outliers final: 18 residues processed: 116 average time/residue: 1.2452 time to fit residues: 159.9586 Evaluate side-chains 116 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL 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 407 CYS Chi-restraints excluded: chain 2 residue 589 PHE 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 278 SER Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 474 VAL 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: 0.7980 chunk 7 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 29 optimal weight: 0.0050 chunk 103 optimal weight: 0.5980 chunk 150 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.216106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.140723 restraints weight = 13251.472| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.42 r_work: 0.3354 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11070 Z= 0.139 Angle : 0.544 9.407 15140 Z= 0.272 Chirality : 0.041 0.153 1751 Planarity : 0.004 0.039 1991 Dihedral : 4.909 38.018 1725 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.21 % Allowed : 15.77 % Favored : 82.02 % 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: 0.36 (0.22), residues: 1515 helix: 2.20 (0.20), residues: 701 sheet: -1.07 (0.40), residues: 150 loop : -1.70 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 2 487 HIS 0.011 0.001 HIS 3 498 PHE 0.013 0.001 PHE 2 621 TYR 0.014 0.001 TYR 3 256 ARG 0.008 0.000 ARG 2 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 2) link_NAG-ASN : angle 1.34317 ( 6) hydrogen bonds : bond 0.03175 ( 524) hydrogen bonds : angle 3.47189 ( 1542) SS BOND : bond 0.00239 ( 18) SS BOND : angle 1.04317 ( 36) covalent geometry : bond 0.00323 (11050) covalent geometry : angle 0.54138 (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 114 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: 2 258 LEU cc_start: 0.7468 (mt) cc_final: 0.7108 (mt) REVERT: 2 411 ARG cc_start: 0.8021 (mmt-90) cc_final: 0.7233 (mmt180) REVERT: 2 414 ASN cc_start: 0.7395 (p0) cc_final: 0.7152 (p0) REVERT: 2 524 PRO cc_start: 0.6912 (Cg_exo) cc_final: 0.6698 (Cg_endo) REVERT: 2 589 PHE cc_start: 0.6712 (OUTLIER) cc_final: 0.6501 (p90) REVERT: 3 235 ARG cc_start: 0.6970 (mtm110) cc_final: 0.6695 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6859 (mm) REVERT: 3 275 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: 3 363 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6482 (mp) REVERT: 3 488 GLU cc_start: 0.8187 (tp30) cc_final: 0.7900 (tp30) outliers start: 21 outliers final: 16 residues processed: 109 average time/residue: 0.9079 time to fit residues: 109.9929 Evaluate side-chains 113 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL 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 407 CYS Chi-restraints excluded: chain 2 residue 589 PHE 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 391 MET Chi-restraints excluded: chain 3 residue 474 VAL 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: 2.9990 chunk 81 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 67 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 = 0.4473 r_free = 0.4473 target = 0.211808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133903 restraints weight = 13041.763| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.03 r_work: 0.3347 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11070 Z= 0.237 Angle : 0.629 9.423 15140 Z= 0.317 Chirality : 0.044 0.168 1751 Planarity : 0.004 0.040 1991 Dihedral : 5.651 50.902 1725 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.52 % Allowed : 15.46 % Favored : 82.02 % 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: 0.15 (0.22), residues: 1515 helix: 2.01 (0.20), residues: 704 sheet: -1.25 (0.39), residues: 160 loop : -1.79 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 2 487 HIS 0.012 0.001 HIS 3 498 PHE 0.017 0.002 PHE 2 189 TYR 0.018 0.002 TYR 3 256 ARG 0.008 0.000 ARG 2 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 2) link_NAG-ASN : angle 1.81793 ( 6) hydrogen bonds : bond 0.03896 ( 524) hydrogen bonds : angle 3.65153 ( 1542) SS BOND : bond 0.00521 ( 18) SS BOND : angle 1.32362 ( 36) covalent geometry : bond 0.00568 (11050) covalent geometry : angle 0.62569 (15098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10548.15 seconds wall clock time: 183 minutes 15.67 seconds (10995.67 seconds total)