Starting phenix.real_space_refine on Thu Sep 18 08:12:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nhn_49417/09_2025/9nhn_49417.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nhn_49417/09_2025/9nhn_49417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nhn_49417/09_2025/9nhn_49417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nhn_49417/09_2025/9nhn_49417.map" model { file = "/net/cci-nas-00/data/ceres_data/9nhn_49417/09_2025/9nhn_49417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nhn_49417/09_2025/9nhn_49417.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 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 103 5.16 5 C 9393 2.51 5 N 2535 2.21 5 O 3033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15064 Number of models: 1 Model: "" Number of chains: 20 Chain: "H" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 635 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'TRANS': 122} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'UNK:plan-1': 119} Unresolved non-hydrogen planarities: 119 Chain: "L" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 522 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'TRANS': 100} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'UNK:plan-1': 97} Unresolved non-hydrogen planarities: 97 Chain: "C" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3390 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 3 Chain: "D" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 923 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "A" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3390 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 3 Chain: "B" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 923 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3390 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 3 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 990 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.29, per 1000 atoms: 0.22 Number of scatterers: 15064 At special positions: 0 Unit cell: (120.75, 127.65, 143.75, 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 103 16.00 O 3033 8.00 N 2535 7.00 C 9393 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 94 " distance=2.06 Simple disulfide: pdb=" SG CYS L 20 " - pdb=" SG CYS L 83 " distance=2.06 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.02 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS B 663 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 663 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.19 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=1.86 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.06 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS F 663 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.06 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.05 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " NAG J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " NAG M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 230 " " NAG A 606 " - " ASN A 289 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 332 " " NAG A 609 " - " ASN A 386 " " NAG A 610 " - " ASN A 442 " " NAG A 611 " - " ASN A 448 " " NAG A 612 " - " ASN A 88 " " NAG A 613 " - " ASN A 133 " " NAG A 614 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 130 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 197 " " NAG C 604 " - " ASN C 230 " " NAG C 605 " - " ASN C 289 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 332 " " NAG C 608 " - " ASN C 386 " " NAG C 609 " - " ASN C 442 " " NAG C 610 " - " ASN C 448 " " NAG C 611 " - " ASN C 133 " " NAG D 701 " - " ASN D 616 " " NAG D 702 " - " ASN D 637 " " NAG D 703 " - " ASN D 611 " " NAG D 704 " - " ASN D 656 " " NAG E 601 " - " ASN E 130 " " NAG E 602 " - " ASN E 156 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 230 " " NAG E 605 " - " ASN E 289 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 332 " " NAG E 608 " - " ASN E 442 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 88 " " NAG E 611 " - " ASN E 386 " " NAG E 612 " - " ASN E 392 " " NAG E 613 " - " ASN E 339 " " NAG E 614 " - " ASN E 133 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 616 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN C 241 " " NAG I 1 " - " ASN C 262 " " NAG J 1 " - " ASN A 241 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN E 241 " " NAG N 1 " - " ASN E 262 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 557.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3542 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 30 sheets defined 24.6% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'H' and resid 60 through 63 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.580A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.261A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 537 Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 657 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.751A pdb=" N ASN A 98 " --> pdb=" O MET A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.938A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 638 through 659 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.067A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.902A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.940A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 636 through 639 Processing helix chain 'F' and resid 640 through 656 Processing sheet with id=AA1, first strand: chain 'H' and resid 16 through 23 removed outlier: 4.269A pdb=" N UNK H 16 " --> pdb=" O UNK H 83 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N UNK H 83 " --> pdb=" O UNK H 16 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N UNK H 78 " --> pdb=" O UNK H 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 35 through 37 removed outlier: 3.854A pdb=" N UNK H 93 " --> pdb=" O UNK H 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 48 through 49 Processing sheet with id=AA4, first strand: chain 'L' and resid 16 through 20 Processing sheet with id=AA5, first strand: chain 'L' and resid 38 through 41 removed outlier: 8.089A pdb=" N UNK L 38 " --> pdb=" O UNK L 34 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N UNK L 34 " --> pdb=" O UNK L 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.148A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.371A pdb=" N ILE C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 132 through 136 removed outlier: 10.570A pdb=" N THR C 132 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N GLY C 144 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA C 134 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB4, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 330 through 334 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 334 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 467 through 469 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 300 through 312 removed outlier: 4.278A pdb=" N GLN C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N THR C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR C 320 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.464A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.821A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AC1, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AC2, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.502A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 285 through 308 removed outlier: 6.486A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323A current: chain 'A' and resid 382 through 385 removed outlier: 4.053A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.836A pdb=" N ASN A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N PHE A 468 " --> pdb=" O ASN A 358 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.149A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.722A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AD1, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AD2, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.953A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 287 current: chain 'E' and resid 315 through 324 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 324 current: chain 'E' and resid 381 through 385 removed outlier: 4.536A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 413 through 421 current: chain 'E' and resid 467 through 470 442 hydrogen bonds defined for protein. 1173 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: 2.92 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 4010 1.33 - 1.48: 4799 1.48 - 1.62: 6395 1.62 - 1.77: 29 1.77 - 1.92: 106 Bond restraints: 15339 Sorted by residual: bond pdb=" CD2 TRP E 395 " pdb=" CE3 TRP E 395 " ideal model delta sigma weight residual 1.398 1.505 -0.107 1.60e-02 3.91e+03 4.49e+01 bond pdb=" CZ2 TRP E 395 " pdb=" CH2 TRP E 395 " ideal model delta sigma weight residual 1.368 1.493 -0.125 1.90e-02 2.77e+03 4.36e+01 bond pdb=" CB LEU F 520 " pdb=" CG LEU F 520 " ideal model delta sigma weight residual 1.530 1.658 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" CZ2 TRP C 395 " pdb=" CH2 TRP C 395 " ideal model delta sigma weight residual 1.368 1.477 -0.109 1.90e-02 2.77e+03 3.32e+01 bond pdb=" CD2 TRP C 395 " pdb=" CE3 TRP C 395 " ideal model delta sigma weight residual 1.398 1.490 -0.092 1.60e-02 3.91e+03 3.29e+01 ... (remaining 15334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 18555 2.60 - 5.21: 2067 5.21 - 7.81: 243 7.81 - 10.41: 23 10.41 - 13.02: 3 Bond angle restraints: 20891 Sorted by residual: angle pdb=" N ARG E 476 " pdb=" CA ARG E 476 " pdb=" C ARG E 476 " ideal model delta sigma weight residual 114.04 101.24 12.80 1.24e+00 6.50e-01 1.07e+02 angle pdb=" N ARG E 327 " pdb=" CA ARG E 327 " pdb=" C ARG E 327 " ideal model delta sigma weight residual 114.39 101.72 12.67 1.45e+00 4.76e-01 7.64e+01 angle pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 119.82 127.77 -7.95 9.80e-01 1.04e+00 6.59e+01 angle pdb=" N ILE F 641 " pdb=" CA ILE F 641 " pdb=" C ILE F 641 " ideal model delta sigma weight residual 111.45 103.91 7.54 9.30e-01 1.16e+00 6.57e+01 angle pdb=" C GLY A 312 " pdb=" N PRO A 313 " pdb=" CA PRO A 313 " ideal model delta sigma weight residual 119.47 128.81 -9.34 1.16e+00 7.43e-01 6.48e+01 ... (remaining 20886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 9725 21.06 - 42.12: 215 42.12 - 63.18: 60 63.18 - 84.24: 34 84.24 - 105.30: 17 Dihedral angle restraints: 10051 sinusoidal: 4607 harmonic: 5444 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual 93.00 173.82 -80.82 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 73 " pdb=" CB CYS A 73 " ideal model delta sinusoidal sigma weight residual 93.00 22.93 70.07 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS D 663 " pdb=" SG CYS D 663 " pdb=" SG CYS E 501 " pdb=" CB CYS E 501 " ideal model delta sinusoidal sigma weight residual 93.00 156.20 -63.20 1 1.00e+01 1.00e-02 5.27e+01 ... (remaining 10048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1790 0.105 - 0.210: 522 0.210 - 0.315: 173 0.315 - 0.420: 86 0.420 - 0.525: 35 Chirality restraints: 2606 Sorted by residual: chirality pdb=" C1 NAG M 3 " pdb=" O4 NAG M 2 " pdb=" C2 NAG M 3 " pdb=" O5 NAG M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.21e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.21e+02 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.16e+02 ... (remaining 2603 not shown) Planarity restraints: 2645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 702 " 0.330 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG F 702 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG F 702 " 0.101 2.00e-02 2.50e+03 pdb=" N2 NAG F 702 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG F 702 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 703 " 0.278 2.00e-02 2.50e+03 2.41e-01 7.29e+02 pdb=" C7 NAG F 703 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG F 703 " 0.005 2.00e-02 2.50e+03 pdb=" N2 NAG F 703 " -0.417 2.00e-02 2.50e+03 pdb=" O7 NAG F 703 " 0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 230 " -0.081 2.00e-02 2.50e+03 8.46e-02 8.94e+01 pdb=" CG ASN E 230 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN E 230 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN E 230 " 0.129 2.00e-02 2.50e+03 pdb=" C1 NAG E 604 " -0.104 2.00e-02 2.50e+03 ... (remaining 2642 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4814 2.85 - 3.36: 14042 3.36 - 3.87: 24779 3.87 - 4.39: 28851 4.39 - 4.90: 45351 Nonbonded interactions: 117837 Sorted by model distance: nonbonded pdb=" O THR C 162 " pdb=" OG1 THR C 163 " model vdw 2.332 3.040 nonbonded pdb=" N ARG E 327 " pdb=" N GLU E 328 " model vdw 2.332 2.560 nonbonded pdb=" NZ LYS B 655 " pdb=" OD2 ASP B 659 " model vdw 2.366 3.120 nonbonded pdb=" NZ LYS E 46 " pdb=" OD2 ASP F 632 " model vdw 2.380 3.120 nonbonded pdb=" OG SER E 393 " pdb=" N THR E 394 " model vdw 2.381 3.120 ... (remaining 117832 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 611) selection = chain 'C' selection = (chain 'E' and resid 32 through 611) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 521 through 701) selection = (chain 'F' and (resid 521 through 539 or resid 568 through 701)) } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 7.160 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.670 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 : 0.022 0.175 15439 Z= 1.151 Angle : 1.739 15.164 21156 Z= 1.104 Chirality : 0.136 0.525 2606 Planarity : 0.012 0.287 2592 Dihedral : 11.409 105.298 6404 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.20), residues: 1620 helix: 0.07 (0.24), residues: 384 sheet: 0.69 (0.26), residues: 377 loop : 0.40 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 469 TYR 0.061 0.007 TYR B 638 PHE 0.034 0.006 PHE A 376 TRP 0.074 0.011 TRP A 479 HIS 0.015 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.02128 (15339) covalent geometry : angle 1.70843 (20891) SS BOND : bond 0.04296 ( 35) SS BOND : angle 2.83854 ( 70) hydrogen bonds : bond 0.15081 ( 442) hydrogen bonds : angle 7.18411 ( 1173) link_BETA1-4 : bond 0.06994 ( 12) link_BETA1-4 : angle 4.80771 ( 36) link_NAG-ASN : bond 0.07761 ( 53) link_NAG-ASN : angle 3.20188 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 ASN cc_start: 0.8291 (p0) cc_final: 0.7927 (p0) REVERT: C 256 SER cc_start: 0.9314 (p) cc_final: 0.9040 (t) REVERT: C 297 THR cc_start: 0.9126 (m) cc_final: 0.8668 (p) REVERT: C 395 TRP cc_start: 0.8262 (m100) cc_final: 0.7803 (m100) REVERT: D 584 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8008 (tm-30) REVERT: D 623 TRP cc_start: 0.9119 (m100) cc_final: 0.8857 (m-10) REVERT: D 627 THR cc_start: 0.8729 (p) cc_final: 0.8059 (p) REVERT: D 653 GLN cc_start: 0.8970 (tt0) cc_final: 0.8766 (tt0) REVERT: A 347 LYS cc_start: 0.8687 (mttt) cc_final: 0.8135 (tppt) REVERT: A 381 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6828 (mm-30) REVERT: A 491 ILE cc_start: 0.9120 (mt) cc_final: 0.8859 (tt) REVERT: B 626 MET cc_start: 0.4514 (mmp) cc_final: 0.4168 (mtt) REVERT: E 42 VAL cc_start: 0.9498 (t) cc_final: 0.9278 (p) REVERT: F 586 TYR cc_start: 0.9270 (t80) cc_final: 0.8952 (t80) REVERT: F 595 ILE cc_start: 0.8961 (tt) cc_final: 0.8337 (tp) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.1332 time to fit residues: 78.8701 Evaluate side-chains 192 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS D 585 HIS D 591 GLN A 249 HIS ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.109101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090285 restraints weight = 40056.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092924 restraints weight = 22605.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.093908 restraints weight = 15394.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.094483 restraints weight = 13248.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.094653 restraints weight = 12250.385| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15439 Z= 0.178 Angle : 0.807 12.741 21156 Z= 0.392 Chirality : 0.048 0.309 2606 Planarity : 0.004 0.053 2592 Dihedral : 8.352 74.825 3319 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.96 % Allowed : 8.65 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.21), residues: 1620 helix: 1.62 (0.28), residues: 358 sheet: 0.08 (0.25), residues: 393 loop : -0.12 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 273 TYR 0.018 0.002 TYR A 486 PHE 0.020 0.002 PHE A 353 TRP 0.026 0.002 TRP A 479 HIS 0.012 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00396 (15339) covalent geometry : angle 0.74133 (20891) SS BOND : bond 0.00249 ( 35) SS BOND : angle 1.07765 ( 70) hydrogen bonds : bond 0.04982 ( 442) hydrogen bonds : angle 5.31294 ( 1173) link_BETA1-4 : bond 0.00960 ( 12) link_BETA1-4 : angle 3.10642 ( 36) link_NAG-ASN : bond 0.00576 ( 53) link_NAG-ASN : angle 3.41896 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 ASN cc_start: 0.8447 (m-40) cc_final: 0.8191 (m110) REVERT: C 195 ASN cc_start: 0.7992 (p0) cc_final: 0.7451 (p0) REVERT: C 297 THR cc_start: 0.9259 (m) cc_final: 0.8850 (p) REVERT: D 623 TRP cc_start: 0.9125 (m100) cc_final: 0.8679 (m-10) REVERT: D 653 GLN cc_start: 0.8910 (tt0) cc_final: 0.8701 (tt0) REVERT: A 347 LYS cc_start: 0.8585 (mttt) cc_final: 0.8024 (tppt) REVERT: B 596 TRP cc_start: 0.9240 (m-10) cc_final: 0.8994 (m-10) REVERT: B 626 MET cc_start: 0.4403 (mmp) cc_final: 0.3929 (mtt) REVERT: B 631 TRP cc_start: 0.8293 (t60) cc_final: 0.8018 (t60) REVERT: E 303 THR cc_start: 0.8507 (p) cc_final: 0.8169 (p) REVERT: E 425 ASN cc_start: 0.7710 (p0) cc_final: 0.7470 (p0) REVERT: F 661 LEU cc_start: 0.8110 (mt) cc_final: 0.7642 (tp) outliers start: 29 outliers final: 15 residues processed: 250 average time/residue: 0.1131 time to fit residues: 43.1322 Evaluate side-chains 206 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 624 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 23 optimal weight: 0.0270 chunk 156 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 640 GLN D 651 ASN E 80 ASN E 195 ASN E 355 HIS F 540 GLN F 591 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.098731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.079517 restraints weight = 40859.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.082398 restraints weight = 24783.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.083783 restraints weight = 15021.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.084567 restraints weight = 11914.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.084786 restraints weight = 11053.940| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15439 Z= 0.169 Angle : 0.686 11.646 21156 Z= 0.333 Chirality : 0.046 0.287 2606 Planarity : 0.004 0.046 2592 Dihedral : 6.755 56.249 3319 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.69 % Allowed : 10.48 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.21), residues: 1620 helix: 1.96 (0.29), residues: 341 sheet: -0.03 (0.26), residues: 366 loop : -0.32 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 273 TYR 0.017 0.002 TYR F 638 PHE 0.015 0.002 PHE E 53 TRP 0.021 0.002 TRP A 69 HIS 0.010 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00384 (15339) covalent geometry : angle 0.63820 (20891) SS BOND : bond 0.00279 ( 35) SS BOND : angle 0.89551 ( 70) hydrogen bonds : bond 0.04043 ( 442) hydrogen bonds : angle 5.01212 ( 1173) link_BETA1-4 : bond 0.00678 ( 12) link_BETA1-4 : angle 2.51465 ( 36) link_NAG-ASN : bond 0.00585 ( 53) link_NAG-ASN : angle 2.69273 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 187 ASN cc_start: 0.8500 (m-40) cc_final: 0.8267 (m110) REVERT: C 195 ASN cc_start: 0.8021 (p0) cc_final: 0.7435 (p0) REVERT: C 280 ASN cc_start: 0.7257 (p0) cc_final: 0.7017 (p0) REVERT: C 297 THR cc_start: 0.9400 (m) cc_final: 0.9085 (p) REVERT: D 595 ILE cc_start: 0.9589 (tp) cc_final: 0.9192 (tp) REVERT: D 623 TRP cc_start: 0.9262 (m100) cc_final: 0.8557 (m-10) REVERT: D 650 GLN cc_start: 0.9062 (tp40) cc_final: 0.8360 (tp40) REVERT: A 347 LYS cc_start: 0.8707 (mttt) cc_final: 0.8077 (tppt) REVERT: B 586 TYR cc_start: 0.9012 (t80) cc_final: 0.8800 (t80) REVERT: B 602 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8211 (mp) REVERT: B 626 MET cc_start: 0.4819 (mmp) cc_final: 0.3926 (mtt) REVERT: B 631 TRP cc_start: 0.8387 (t60) cc_final: 0.7999 (t60) REVERT: B 651 ASN cc_start: 0.8919 (m-40) cc_final: 0.8602 (m-40) REVERT: E 246 GLN cc_start: 0.8012 (tt0) cc_final: 0.7732 (tp40) REVERT: E 303 THR cc_start: 0.8639 (p) cc_final: 0.8345 (p) REVERT: E 425 ASN cc_start: 0.7865 (p0) cc_final: 0.7442 (p0) REVERT: E 435 TYR cc_start: 0.8982 (t80) cc_final: 0.8552 (t80) REVERT: F 577 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8691 (tm-30) REVERT: F 661 LEU cc_start: 0.7965 (mt) cc_final: 0.7512 (tp) outliers start: 25 outliers final: 15 residues processed: 215 average time/residue: 0.1125 time to fit residues: 37.5565 Evaluate side-chains 195 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain F residue 573 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 25 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 141 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.097923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078354 restraints weight = 41146.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.080651 restraints weight = 24030.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082190 restraints weight = 16848.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083292 restraints weight = 13282.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.083989 restraints weight = 11169.585| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15439 Z= 0.146 Angle : 0.642 11.712 21156 Z= 0.311 Chirality : 0.045 0.288 2606 Planarity : 0.003 0.051 2592 Dihedral : 5.828 54.975 3319 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.62 % Allowed : 11.70 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.21), residues: 1620 helix: 1.98 (0.29), residues: 341 sheet: -0.15 (0.25), residues: 395 loop : -0.35 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 504 TYR 0.014 0.002 TYR B 643 PHE 0.014 0.001 PHE E 53 TRP 0.022 0.002 TRP E 69 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00335 (15339) covalent geometry : angle 0.59637 (20891) SS BOND : bond 0.00256 ( 35) SS BOND : angle 0.81806 ( 70) hydrogen bonds : bond 0.03709 ( 442) hydrogen bonds : angle 4.82309 ( 1173) link_BETA1-4 : bond 0.00538 ( 12) link_BETA1-4 : angle 2.26260 ( 36) link_NAG-ASN : bond 0.00446 ( 53) link_NAG-ASN : angle 2.58825 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 TRP cc_start: 0.6184 (m100) cc_final: 0.4917 (m100) REVERT: C 187 ASN cc_start: 0.8458 (m-40) cc_final: 0.8217 (m110) REVERT: C 195 ASN cc_start: 0.7967 (p0) cc_final: 0.7522 (p0) REVERT: C 297 THR cc_start: 0.9378 (m) cc_final: 0.9114 (p) REVERT: D 595 ILE cc_start: 0.9539 (tp) cc_final: 0.9151 (tp) REVERT: D 623 TRP cc_start: 0.9229 (m100) cc_final: 0.8430 (m-10) REVERT: D 627 THR cc_start: 0.8529 (p) cc_final: 0.7897 (p) REVERT: A 347 LYS cc_start: 0.8678 (mttt) cc_final: 0.8098 (tppt) REVERT: B 602 LEU cc_start: 0.8717 (pt) cc_final: 0.8284 (mt) REVERT: B 626 MET cc_start: 0.4807 (mmp) cc_final: 0.3977 (mtt) REVERT: B 651 ASN cc_start: 0.8936 (m-40) cc_final: 0.8600 (m-40) REVERT: E 39 TYR cc_start: 0.8860 (m-80) cc_final: 0.8626 (m-80) REVERT: E 303 THR cc_start: 0.8615 (p) cc_final: 0.8326 (p) REVERT: E 425 ASN cc_start: 0.7847 (p0) cc_final: 0.7401 (p0) REVERT: E 435 TYR cc_start: 0.9077 (t80) cc_final: 0.8613 (t80) REVERT: F 577 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8698 (tm-30) REVERT: F 595 ILE cc_start: 0.8741 (tp) cc_final: 0.7921 (tp) REVERT: F 647 GLU cc_start: 0.8099 (tp30) cc_final: 0.7660 (tp30) REVERT: F 661 LEU cc_start: 0.8092 (mt) cc_final: 0.7717 (tp) outliers start: 24 outliers final: 14 residues processed: 218 average time/residue: 0.1044 time to fit residues: 35.6669 Evaluate side-chains 188 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 649 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 45 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.075250 restraints weight = 40692.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.078271 restraints weight = 25584.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.079344 restraints weight = 16174.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.079325 restraints weight = 12786.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079894 restraints weight = 13139.421| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 15439 Z= 0.288 Angle : 0.813 18.326 21156 Z= 0.388 Chirality : 0.052 0.920 2606 Planarity : 0.005 0.053 2592 Dihedral : 6.222 56.245 3319 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.70 % Allowed : 11.22 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.21), residues: 1620 helix: 1.70 (0.29), residues: 341 sheet: -0.25 (0.25), residues: 386 loop : -0.65 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 298 TYR 0.031 0.003 TYR B 643 PHE 0.019 0.002 PHE A 376 TRP 0.042 0.003 TRP B 631 HIS 0.006 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00658 (15339) covalent geometry : angle 0.75880 (20891) SS BOND : bond 0.00496 ( 35) SS BOND : angle 1.08228 ( 70) hydrogen bonds : bond 0.04410 ( 442) hydrogen bonds : angle 5.08068 ( 1173) link_BETA1-4 : bond 0.00576 ( 12) link_BETA1-4 : angle 2.44279 ( 36) link_NAG-ASN : bond 0.00522 ( 53) link_NAG-ASN : angle 3.21642 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: C 111 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8884 (tt) REVERT: C 195 ASN cc_start: 0.8169 (p0) cc_final: 0.7674 (p0) REVERT: C 305 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 347 LYS cc_start: 0.8798 (mttt) cc_final: 0.8094 (tppt) REVERT: B 602 LEU cc_start: 0.8866 (pt) cc_final: 0.8254 (mt) REVERT: B 626 MET cc_start: 0.5417 (mmp) cc_final: 0.4459 (mtt) REVERT: B 634 GLU cc_start: 0.7622 (pt0) cc_final: 0.7171 (tm-30) REVERT: B 643 TYR cc_start: 0.9273 (m-80) cc_final: 0.9033 (m-80) REVERT: B 651 ASN cc_start: 0.9000 (m-40) cc_final: 0.8631 (m-40) REVERT: E 425 ASN cc_start: 0.7962 (p0) cc_final: 0.7502 (p0) REVERT: E 435 TYR cc_start: 0.9193 (t80) cc_final: 0.8939 (t80) REVERT: F 577 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8818 (tm-30) REVERT: F 591 GLN cc_start: 0.8206 (tt0) cc_final: 0.7941 (tt0) REVERT: F 648 GLU cc_start: 0.8151 (pp20) cc_final: 0.7878 (pp20) REVERT: F 661 LEU cc_start: 0.8129 (mt) cc_final: 0.7740 (tp) outliers start: 40 outliers final: 24 residues processed: 197 average time/residue: 0.1040 time to fit residues: 31.7092 Evaluate side-chains 177 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain F residue 573 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN C 229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.077378 restraints weight = 39971.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079967 restraints weight = 25151.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.081916 restraints weight = 16193.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082210 restraints weight = 11794.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.082604 restraints weight = 11799.146| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15439 Z= 0.160 Angle : 0.683 16.245 21156 Z= 0.330 Chirality : 0.052 1.191 2606 Planarity : 0.004 0.058 2592 Dihedral : 5.932 54.421 3319 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.03 % Allowed : 13.05 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.21), residues: 1620 helix: 1.91 (0.29), residues: 342 sheet: -0.18 (0.25), residues: 391 loop : -0.65 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 504 TYR 0.022 0.002 TYR B 643 PHE 0.012 0.001 PHE E 53 TRP 0.042 0.002 TRP B 628 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00366 (15339) covalent geometry : angle 0.63374 (20891) SS BOND : bond 0.00473 ( 35) SS BOND : angle 1.22873 ( 70) hydrogen bonds : bond 0.03792 ( 442) hydrogen bonds : angle 4.75564 ( 1173) link_BETA1-4 : bond 0.00418 ( 12) link_BETA1-4 : angle 1.68667 ( 36) link_NAG-ASN : bond 0.00363 ( 53) link_NAG-ASN : angle 2.81200 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 ASN cc_start: 0.8158 (p0) cc_final: 0.7694 (p0) REVERT: C 305 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8632 (p) REVERT: D 584 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7517 (mt-10) REVERT: D 595 ILE cc_start: 0.9508 (tp) cc_final: 0.9161 (tp) REVERT: A 347 LYS cc_start: 0.8755 (mttt) cc_final: 0.8047 (tppt) REVERT: B 602 LEU cc_start: 0.8968 (pt) cc_final: 0.8394 (mt) REVERT: B 626 MET cc_start: 0.5189 (mmp) cc_final: 0.4106 (mtm) REVERT: B 634 GLU cc_start: 0.7455 (pt0) cc_final: 0.7178 (tm-30) REVERT: B 647 GLU cc_start: 0.8531 (tt0) cc_final: 0.8200 (tm-30) REVERT: B 648 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8254 (mm-30) REVERT: E 42 VAL cc_start: 0.9446 (t) cc_final: 0.9140 (p) REVERT: E 303 THR cc_start: 0.8695 (p) cc_final: 0.8464 (p) REVERT: E 425 ASN cc_start: 0.7785 (p0) cc_final: 0.7381 (p0) REVERT: E 435 TYR cc_start: 0.9183 (t80) cc_final: 0.8974 (t80) REVERT: F 577 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8736 (tm-30) REVERT: F 591 GLN cc_start: 0.8189 (tt0) cc_final: 0.7922 (tt0) REVERT: F 648 GLU cc_start: 0.8044 (pp20) cc_final: 0.7813 (pp20) REVERT: F 661 LEU cc_start: 0.8140 (mt) cc_final: 0.7769 (tp) outliers start: 30 outliers final: 23 residues processed: 185 average time/residue: 0.1146 time to fit residues: 32.9086 Evaluate side-chains 177 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 65 optimal weight: 0.0970 chunk 155 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.096974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078681 restraints weight = 39333.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081436 restraints weight = 24255.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.083299 restraints weight = 15341.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083167 restraints weight = 11200.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.083494 restraints weight = 11787.939| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15439 Z= 0.132 Angle : 0.652 13.912 21156 Z= 0.313 Chirality : 0.049 1.006 2606 Planarity : 0.004 0.055 2592 Dihedral : 5.652 54.895 3319 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.69 % Allowed : 13.39 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.21), residues: 1620 helix: 2.07 (0.30), residues: 341 sheet: -0.07 (0.25), residues: 390 loop : -0.62 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 480 TYR 0.028 0.002 TYR B 643 PHE 0.014 0.001 PHE C 317 TRP 0.057 0.002 TRP E 69 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00297 (15339) covalent geometry : angle 0.60644 (20891) SS BOND : bond 0.00240 ( 35) SS BOND : angle 1.02089 ( 70) hydrogen bonds : bond 0.03574 ( 442) hydrogen bonds : angle 4.60581 ( 1173) link_BETA1-4 : bond 0.00504 ( 12) link_BETA1-4 : angle 1.58765 ( 36) link_NAG-ASN : bond 0.00433 ( 53) link_NAG-ASN : angle 2.68758 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8840 (tt) REVERT: C 195 ASN cc_start: 0.8148 (p0) cc_final: 0.7687 (p0) REVERT: C 280 ASN cc_start: 0.7493 (p0) cc_final: 0.7277 (p0) REVERT: D 530 MET cc_start: 0.8091 (mtm) cc_final: 0.7434 (mpp) REVERT: D 584 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7453 (mt-10) REVERT: D 595 ILE cc_start: 0.9527 (tp) cc_final: 0.9171 (tp) REVERT: A 154 MET cc_start: 0.7096 (mmp) cc_final: 0.6770 (mmp) REVERT: A 347 LYS cc_start: 0.8729 (mttt) cc_final: 0.8053 (tppt) REVERT: B 602 LEU cc_start: 0.8989 (pt) cc_final: 0.8382 (mt) REVERT: B 626 MET cc_start: 0.5175 (mmp) cc_final: 0.4097 (mtt) REVERT: B 634 GLU cc_start: 0.7398 (pt0) cc_final: 0.7185 (tm-30) REVERT: B 647 GLU cc_start: 0.8506 (tt0) cc_final: 0.8186 (tm-30) REVERT: B 648 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8221 (mm-30) REVERT: B 653 GLN cc_start: 0.9214 (tt0) cc_final: 0.8736 (tm-30) REVERT: B 657 GLU cc_start: 0.8705 (mm-30) cc_final: 0.7878 (mm-30) REVERT: E 42 VAL cc_start: 0.9445 (t) cc_final: 0.9140 (p) REVERT: E 303 THR cc_start: 0.8659 (p) cc_final: 0.8429 (p) REVERT: E 425 ASN cc_start: 0.7805 (p0) cc_final: 0.7415 (p0) REVERT: E 435 TYR cc_start: 0.9183 (t80) cc_final: 0.8973 (t80) REVERT: F 577 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8736 (tm-30) REVERT: F 625 ASN cc_start: 0.6880 (p0) cc_final: 0.6661 (p0) REVERT: F 648 GLU cc_start: 0.7951 (pp20) cc_final: 0.7727 (pp20) REVERT: F 661 LEU cc_start: 0.8201 (mt) cc_final: 0.7840 (tp) outliers start: 25 outliers final: 18 residues processed: 193 average time/residue: 0.1081 time to fit residues: 32.4872 Evaluate side-chains 182 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 79 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 118 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079329 restraints weight = 40131.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.082583 restraints weight = 24440.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083690 restraints weight = 15036.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083734 restraints weight = 11427.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.084304 restraints weight = 11894.388| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15439 Z= 0.123 Angle : 0.634 12.505 21156 Z= 0.307 Chirality : 0.048 0.833 2606 Planarity : 0.004 0.054 2592 Dihedral : 5.490 55.159 3319 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.42 % Allowed : 14.40 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.21), residues: 1620 helix: 2.16 (0.30), residues: 342 sheet: -0.13 (0.25), residues: 416 loop : -0.56 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 480 TYR 0.036 0.002 TYR B 643 PHE 0.014 0.001 PHE C 317 TRP 0.063 0.002 TRP B 628 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00278 (15339) covalent geometry : angle 0.58995 (20891) SS BOND : bond 0.00219 ( 35) SS BOND : angle 0.87260 ( 70) hydrogen bonds : bond 0.03421 ( 442) hydrogen bonds : angle 4.51462 ( 1173) link_BETA1-4 : bond 0.00454 ( 12) link_BETA1-4 : angle 1.53189 ( 36) link_NAG-ASN : bond 0.00365 ( 53) link_NAG-ASN : angle 2.62705 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7788 (mt-10) REVERT: C 195 ASN cc_start: 0.8116 (p0) cc_final: 0.7655 (p0) REVERT: D 584 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7453 (mt-10) REVERT: D 595 ILE cc_start: 0.9535 (tp) cc_final: 0.9200 (tp) REVERT: D 648 GLU cc_start: 0.8247 (tm-30) cc_final: 0.8016 (tp30) REVERT: A 154 MET cc_start: 0.7020 (mmp) cc_final: 0.6559 (mmp) REVERT: A 347 LYS cc_start: 0.8655 (mttt) cc_final: 0.8056 (tppt) REVERT: A 492 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7899 (mm-30) REVERT: B 602 LEU cc_start: 0.9001 (pt) cc_final: 0.8403 (mt) REVERT: B 617 LYS cc_start: 0.7972 (mmtp) cc_final: 0.7763 (mmtp) REVERT: B 626 MET cc_start: 0.5021 (mmp) cc_final: 0.3841 (mtm) REVERT: B 634 GLU cc_start: 0.7354 (pt0) cc_final: 0.7138 (tm-30) REVERT: B 647 GLU cc_start: 0.8498 (tt0) cc_final: 0.8188 (tm-30) REVERT: B 648 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8194 (mm-30) REVERT: B 653 GLN cc_start: 0.9197 (tt0) cc_final: 0.8748 (tm-30) REVERT: B 657 GLU cc_start: 0.8638 (mm-30) cc_final: 0.7886 (mm-30) REVERT: E 303 THR cc_start: 0.8665 (p) cc_final: 0.8384 (p) REVERT: E 425 ASN cc_start: 0.7644 (p0) cc_final: 0.7261 (p0) REVERT: E 435 TYR cc_start: 0.9174 (t80) cc_final: 0.8965 (t80) REVERT: F 577 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8679 (tm-30) REVERT: F 625 ASN cc_start: 0.6881 (p0) cc_final: 0.6657 (p0) REVERT: F 648 GLU cc_start: 0.7831 (pp20) cc_final: 0.7623 (pp20) REVERT: F 661 LEU cc_start: 0.8157 (mt) cc_final: 0.7855 (tp) outliers start: 21 outliers final: 19 residues processed: 193 average time/residue: 0.1162 time to fit residues: 34.4156 Evaluate side-chains 184 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 64 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS F 585 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.093662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.075232 restraints weight = 40836.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077795 restraints weight = 25454.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.079255 restraints weight = 16282.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.079303 restraints weight = 12699.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.079536 restraints weight = 12910.968| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 15439 Z= 0.256 Angle : 0.764 15.268 21156 Z= 0.368 Chirality : 0.051 0.821 2606 Planarity : 0.004 0.060 2592 Dihedral : 6.126 55.203 3319 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.03 % Allowed : 14.33 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.21), residues: 1620 helix: 1.98 (0.30), residues: 342 sheet: -0.32 (0.25), residues: 394 loop : -0.80 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 504 TYR 0.028 0.002 TYR B 643 PHE 0.016 0.002 PHE A 376 TRP 0.073 0.003 TRP B 628 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00594 (15339) covalent geometry : angle 0.72352 (20891) SS BOND : bond 0.00392 ( 35) SS BOND : angle 1.09642 ( 70) hydrogen bonds : bond 0.04123 ( 442) hydrogen bonds : angle 4.82939 ( 1173) link_BETA1-4 : bond 0.00364 ( 12) link_BETA1-4 : angle 1.60117 ( 36) link_NAG-ASN : bond 0.00492 ( 53) link_NAG-ASN : angle 2.79330 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8949 (tt) REVERT: C 195 ASN cc_start: 0.8057 (p0) cc_final: 0.7605 (p0) REVERT: A 154 MET cc_start: 0.6841 (mmp) cc_final: 0.6568 (mmp) REVERT: A 347 LYS cc_start: 0.8815 (mttt) cc_final: 0.8088 (tppt) REVERT: B 602 LEU cc_start: 0.9016 (pt) cc_final: 0.8392 (mt) REVERT: B 626 MET cc_start: 0.5617 (mmp) cc_final: 0.4114 (ptp) REVERT: B 634 GLU cc_start: 0.7547 (pt0) cc_final: 0.7213 (tm-30) REVERT: B 651 ASN cc_start: 0.9024 (m-40) cc_final: 0.8609 (m-40) REVERT: B 653 GLN cc_start: 0.9233 (tt0) cc_final: 0.8749 (tm-30) REVERT: B 657 GLU cc_start: 0.8740 (mm-30) cc_final: 0.7990 (mm-30) REVERT: E 425 ASN cc_start: 0.7788 (p0) cc_final: 0.7319 (p0) REVERT: E 435 TYR cc_start: 0.9243 (t80) cc_final: 0.9001 (t80) REVERT: F 540 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7391 (mp-120) REVERT: F 577 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8757 (tm-30) REVERT: F 625 ASN cc_start: 0.6981 (p0) cc_final: 0.6746 (p0) REVERT: F 661 LEU cc_start: 0.8266 (mt) cc_final: 0.7897 (tp) outliers start: 30 outliers final: 21 residues processed: 182 average time/residue: 0.1090 time to fit residues: 30.5541 Evaluate side-chains 175 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 585 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 117 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.076563 restraints weight = 40524.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.079239 restraints weight = 25635.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081430 restraints weight = 16423.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.081383 restraints weight = 11456.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.081848 restraints weight = 11929.720| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15439 Z= 0.165 Angle : 0.688 14.249 21156 Z= 0.333 Chirality : 0.049 0.778 2606 Planarity : 0.004 0.063 2592 Dihedral : 5.945 54.687 3319 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.62 % Allowed : 14.67 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.21), residues: 1620 helix: 2.00 (0.30), residues: 341 sheet: -0.20 (0.25), residues: 392 loop : -0.84 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 504 TYR 0.019 0.002 TYR B 638 PHE 0.012 0.001 PHE C 317 TRP 0.061 0.002 TRP B 628 HIS 0.011 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00380 (15339) covalent geometry : angle 0.64558 (20891) SS BOND : bond 0.00267 ( 35) SS BOND : angle 0.92860 ( 70) hydrogen bonds : bond 0.03804 ( 442) hydrogen bonds : angle 4.68352 ( 1173) link_BETA1-4 : bond 0.00394 ( 12) link_BETA1-4 : angle 1.56858 ( 36) link_NAG-ASN : bond 0.00393 ( 53) link_NAG-ASN : angle 2.71246 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8909 (tt) REVERT: C 195 ASN cc_start: 0.8043 (p0) cc_final: 0.7578 (p0) REVERT: D 584 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7724 (mt-10) REVERT: D 595 ILE cc_start: 0.9515 (tp) cc_final: 0.9188 (tp) REVERT: A 154 MET cc_start: 0.6537 (mmp) cc_final: 0.6206 (mmp) REVERT: A 347 LYS cc_start: 0.8821 (mttt) cc_final: 0.8091 (tppt) REVERT: B 602 LEU cc_start: 0.9091 (pt) cc_final: 0.8502 (mt) REVERT: B 626 MET cc_start: 0.5428 (mmp) cc_final: 0.3884 (ptp) REVERT: B 634 GLU cc_start: 0.7450 (pt0) cc_final: 0.7145 (tm-30) REVERT: B 647 GLU cc_start: 0.8592 (tt0) cc_final: 0.8242 (tm-30) REVERT: B 648 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8231 (mm-30) REVERT: B 652 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8503 (tm-30) REVERT: B 653 GLN cc_start: 0.9190 (tt0) cc_final: 0.8727 (tm-30) REVERT: B 657 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8181 (mm-30) REVERT: E 425 ASN cc_start: 0.7692 (p0) cc_final: 0.7301 (p0) REVERT: E 435 TYR cc_start: 0.9230 (t80) cc_final: 0.8988 (t80) REVERT: F 540 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7319 (mp-120) REVERT: F 577 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8707 (tm-30) REVERT: F 601 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8614 (mtpt) REVERT: F 625 ASN cc_start: 0.6974 (p0) cc_final: 0.6706 (p0) REVERT: F 661 LEU cc_start: 0.8287 (mt) cc_final: 0.7926 (tp) outliers start: 24 outliers final: 21 residues processed: 182 average time/residue: 0.1063 time to fit residues: 29.7475 Evaluate side-chains 180 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 664 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 647 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 39 optimal weight: 0.0060 chunk 129 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.096828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.078617 restraints weight = 39812.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.081366 restraints weight = 24726.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.083255 restraints weight = 15752.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.083082 restraints weight = 11283.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.083595 restraints weight = 11989.147| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15439 Z= 0.122 Angle : 0.650 13.296 21156 Z= 0.313 Chirality : 0.047 0.700 2606 Planarity : 0.004 0.063 2592 Dihedral : 5.608 55.103 3319 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.49 % Allowed : 15.08 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.21), residues: 1620 helix: 2.14 (0.30), residues: 345 sheet: -0.12 (0.25), residues: 420 loop : -0.73 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 504 TYR 0.017 0.001 TYR B 638 PHE 0.012 0.001 PHE C 317 TRP 0.052 0.002 TRP B 628 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00279 (15339) covalent geometry : angle 0.60767 (20891) SS BOND : bond 0.00215 ( 35) SS BOND : angle 0.84374 ( 70) hydrogen bonds : bond 0.03470 ( 442) hydrogen bonds : angle 4.46461 ( 1173) link_BETA1-4 : bond 0.00445 ( 12) link_BETA1-4 : angle 1.56979 ( 36) link_NAG-ASN : bond 0.00405 ( 53) link_NAG-ASN : angle 2.60314 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.34 seconds wall clock time: 38 minutes 26.63 seconds (2306.63 seconds total)