Starting phenix.real_space_refine on Thu Sep 18 07:15:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nho_49418/09_2025/9nho_49418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nho_49418/09_2025/9nho_49418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nho_49418/09_2025/9nho_49418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nho_49418/09_2025/9nho_49418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nho_49418/09_2025/9nho_49418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nho_49418/09_2025/9nho_49418.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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 101 5.16 5 C 9230 2.51 5 N 2494 2.21 5 O 2959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 14784 Number of models: 1 Model: "" Number of chains: 21 Chain: "H" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 625 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'TRANS': 120} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 117 Planarities with less than four sites: {'UNK:plan-1': 117} Unresolved non-hydrogen planarities: 117 Chain: "L" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 532 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 102} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3365 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 3 Chain: "D" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 857 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain breaks: 1 Chain: "A" Number of atoms: 3363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3363 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 3 Chain: "B" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain breaks: 1 Chain: "E" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3371 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 923 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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: "M" 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: "N" 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: "O" 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" 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 Time building chain proxies: 3.71, per 1000 atoms: 0.25 Number of scatterers: 14784 At special positions: 0 Unit cell: (120.75, 128.8, 138, 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 101 16.00 O 2959 8.00 N 2494 7.00 C 9230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 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=2.07 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 500 " - pdb=" SG CYS B 663 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.04 Simple disulfide: pdb=" SG CYS D 663 " - pdb=" SG CYS E 500 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.08 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.08 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 377 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 418 " distance=2.07 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS F 663 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.16 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 K 1 " - " NAG K 2 " " NAG K 2 " - " NAG K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " NAG N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 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 230 " " NAG A 605 " - " ASN A 289 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 332 " " NAG A 608 " - " ASN A 385 " " NAG A 609 " - " ASN A 442 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 88 " " NAG A 612 " - " ASN A 357 " " NAG B 701 " - " ASN B 656 " " NAG B 702 " - " 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 385 " " NAG C 608 " - " ASN C 442 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 138 " " NAG C 611 " - " ASN C 133 " " NAG C 612 " - " ASN C 391 " " NAG C 613 " - " ASN C 339 " " NAG D 701 " - " ASN D 616 " " NAG D 702 " - " ASN D 611 " " 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 133 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN C 241 " " NAG I 1 " - " ASN C 262 " " NAG J 1 " - " ASN C 332 " " NAG K 1 " - " ASN A 241 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN E 241 " " NAG O 1 " - " ASN E 262 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 519.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3494 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 29 sheets defined 25.3% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'H' and resid 53 through 56 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 85 through 89 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.966A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 475 through 483 removed outlier: 4.961A pdb=" N GLU C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 533 Processing helix chain 'D' and resid 572 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 658 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.178A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.834A pdb=" N SER A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 657 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.098A 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 195 through 199 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 475 through 480 Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.713A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 657 removed outlier: 4.385A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 19 through 24 removed outlier: 3.780A pdb=" N UNK H 81 " --> pdb=" O UNK H 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.932A pdb=" N UNK H 50 " --> pdb=" O UNK H 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 91 through 92 Processing sheet with id=AA4, first strand: chain 'H' and resid 102 through 103 removed outlier: 5.424A pdb=" N TYR C 317 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 307 " --> pdb=" O TYR C 317 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N THR C 319 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR C 305 " --> pdb=" O THR C 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.631A pdb=" N TRP L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N UNK L 95 " --> pdb=" O UNK L 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 493 through 497 Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 55 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 169 through 177 removed outlier: 6.654A pdb=" N MET C 154 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 134 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.682A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB3, 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 283 through 298 removed outlier: 7.221A pdb=" N LYS C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER C 334 " --> pdb=" O LYS C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 329 through 334 current: chain 'C' and resid 380 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 380 through 384 current: chain 'C' and resid 464 through 468 Processing sheet with id=AB4, first strand: chain 'A' and resid 493 through 497 removed outlier: 4.862A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB6, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB7, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB8, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AB9, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AC1, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AC2, 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 284 through 304 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 319 through 323 current: chain 'A' and resid 380 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 380 through 384 current: chain 'A' and resid 466 through 469 Processing sheet with id=AC3, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AC4, first strand: chain 'E' and resid 37 through 39 Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.572A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.244A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD1, 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 298 removed outlier: 6.905A pdb=" N LYS E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 329 through 334 current: chain 'E' and resid 381 through 384 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 384 current: chain 'E' and resid 466 through 468 Processing sheet with id=AD2, first strand: chain 'E' and resid 302 through 311 removed outlier: 6.826A pdb=" N THR E 303 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN E 314 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4200 1.33 - 1.48: 4549 1.48 - 1.63: 6174 1.63 - 1.78: 32 1.78 - 1.93: 101 Bond restraints: 15056 Sorted by residual: bond pdb=" CZ2 TRP A 394 " pdb=" CH2 TRP A 394 " ideal model delta sigma weight residual 1.368 1.485 -0.117 1.90e-02 2.77e+03 3.81e+01 bond pdb=" CZ2 TRP D 571 " pdb=" CH2 TRP D 571 " ideal model delta sigma weight residual 1.368 1.485 -0.117 1.90e-02 2.77e+03 3.79e+01 bond pdb=" CD2 TRP D 571 " pdb=" CE3 TRP D 571 " ideal model delta sigma weight residual 1.398 1.494 -0.096 1.60e-02 3.91e+03 3.63e+01 bond pdb=" CB LEU B 520 " pdb=" CG LEU B 520 " ideal model delta sigma weight residual 1.530 1.649 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" CZ2 TRP E 394 " pdb=" CH2 TRP E 394 " ideal model delta sigma weight residual 1.368 1.481 -0.113 1.90e-02 2.77e+03 3.54e+01 ... (remaining 15051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 18129 2.52 - 5.05: 2063 5.05 - 7.57: 284 7.57 - 10.10: 26 10.10 - 12.62: 4 Bond angle restraints: 20506 Sorted by residual: angle pdb=" N ILE E 323 " pdb=" CA ILE E 323 " pdb=" C ILE E 323 " ideal model delta sigma weight residual 110.53 119.30 -8.77 9.40e-01 1.13e+00 8.70e+01 angle pdb=" C ASP F 624 " pdb=" N ASN F 625 " pdb=" CA ASN F 625 " ideal model delta sigma weight residual 120.82 133.23 -12.41 1.47e+00 4.63e-01 7.13e+01 angle pdb=" N THR B 613 " pdb=" CA THR B 613 " pdb=" C THR B 613 " ideal model delta sigma weight residual 114.31 103.44 10.87 1.29e+00 6.01e-01 7.10e+01 angle pdb=" C GLU C 491 " pdb=" N PRO C 492 " pdb=" CA PRO C 492 " ideal model delta sigma weight residual 119.56 127.20 -7.64 1.02e+00 9.61e-01 5.61e+01 angle pdb=" C CYS A 205 " pdb=" N PRO A 206 " pdb=" CA PRO A 206 " ideal model delta sigma weight residual 119.56 127.02 -7.46 1.02e+00 9.61e-01 5.35e+01 ... (remaining 20501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.08: 9525 21.08 - 42.15: 189 42.15 - 63.23: 57 63.23 - 84.31: 35 84.31 - 105.38: 18 Dihedral angle restraints: 9824 sinusoidal: 4457 harmonic: 5367 Sorted by residual: dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 73 " pdb=" CB CYS E 73 " ideal model delta sinusoidal sigma weight residual -86.00 -1.12 -84.88 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -156.81 70.81 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CB CYS D 663 " pdb=" SG CYS D 663 " pdb=" SG CYS E 500 " pdb=" CB CYS E 500 " ideal model delta sinusoidal sigma weight residual 93.00 149.74 -56.74 1 1.00e+01 1.00e-02 4.34e+01 ... (remaining 9821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1703 0.101 - 0.202: 519 0.202 - 0.303: 187 0.303 - 0.404: 78 0.404 - 0.505: 61 Chirality restraints: 2548 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG K 3 " pdb=" O4 NAG K 2 " pdb=" C2 NAG K 3 " pdb=" O5 NAG K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.29e+02 ... (remaining 2545 not shown) Planarity restraints: 2593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.070 2.00e-02 2.50e+03 7.47e-02 6.98e+01 pdb=" CG ASN B 611 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.118 2.00e-02 2.50e+03 pdb=" C1 NAG B 702 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 301 " -0.067 2.00e-02 2.50e+03 7.32e-02 6.70e+01 pdb=" CG ASN C 301 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 301 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN C 301 " 0.118 2.00e-02 2.50e+03 pdb=" C1 NAG C 606 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 230 " -0.069 2.00e-02 2.50e+03 7.10e-02 6.30e+01 pdb=" CG ASN E 230 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN E 230 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN E 230 " 0.108 2.00e-02 2.50e+03 pdb=" C1 NAG E 604 " -0.087 2.00e-02 2.50e+03 ... (remaining 2590 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3637 2.80 - 3.33: 13555 3.33 - 3.85: 24244 3.85 - 4.38: 28557 4.38 - 4.90: 45513 Nonbonded interactions: 115506 Sorted by model distance: nonbonded pdb=" O LEU F 661 " pdb=" OG1 THR F 662 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 498 " model vdw 2.372 3.040 nonbonded pdb=" N THR B 613 " pdb=" N TRP B 614 " model vdw 2.386 2.560 nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.399 2.496 nonbonded pdb=" N ILE C 213 " pdb=" O ILE C 213 " model vdw 2.402 2.496 ... (remaining 115501 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 35 through 376 or (resid 377 and (name N or name CA or nam \ e C or name O or name CB )) or resid 378 through 444 or (resid 445 and (name N o \ r name CA or name C or name O or name CB )) or resid 446 through 610)) selection = (chain 'C' and (resid 35 through 56 or resid 67 through 376 or (resid 377 and (n \ ame N or name CA or name C or name O or name CB )) or resid 378 through 444 or ( \ resid 445 and (name N or name CA or name C or name O or name CB )) or resid 446 \ through 610)) selection = (chain 'E' and (resid 35 through 56 or resid 67 through 610)) } ncs_group { reference = (chain 'B' and (resid 524 through 526 or resid 529 or resid 533 or resid 571 thr \ ough 663 or resid 702)) selection = (chain 'D' and (resid 524 through 526 or resid 529 or resid 533 or resid 571 thr \ ough 663 or resid 702)) selection = (chain 'F' and (resid 531 through 533 or resid 536 or resid 541 or resid 571 thr \ ough 701)) } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'I' 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) selection = (chain 'O' 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: 7.110 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.680 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.021 0.150 15150 Z= 1.123 Angle : 1.730 12.621 20754 Z= 1.100 Chirality : 0.137 0.505 2548 Planarity : 0.009 0.063 2546 Dihedral : 11.397 105.382 6228 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.27 % Allowed : 0.48 % Favored : 99.24 % 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: 0.80 (0.20), residues: 1591 helix: 0.47 (0.26), residues: 347 sheet: 0.69 (0.23), residues: 413 loop : 0.67 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 502 TYR 0.079 0.009 TYR D 638 PHE 0.033 0.006 PHE E 316 TRP 0.075 0.011 TRP C 35 HIS 0.009 0.002 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.02084 (15056) covalent geometry : angle 1.70266 (20506) SS BOND : bond 0.02725 ( 34) SS BOND : angle 3.01757 ( 68) hydrogen bonds : bond 0.13990 ( 448) hydrogen bonds : angle 6.99444 ( 1215) link_BETA1-4 : bond 0.07237 ( 13) link_BETA1-4 : angle 5.04842 ( 39) link_NAG-ASN : bond 0.08118 ( 47) link_NAG-ASN : angle 2.69579 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 354 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8981 (ttt) cc_final: 0.8762 (ttp) REVERT: C 207 LYS cc_start: 0.8391 (pttt) cc_final: 0.7935 (tptp) REVERT: C 432 ARG cc_start: 0.6990 (pmt-80) cc_final: 0.6475 (ppt170) REVERT: C 449 ILE cc_start: 0.9156 (mt) cc_final: 0.8920 (tt) REVERT: C 480 SER cc_start: 0.8828 (p) cc_final: 0.8575 (t) REVERT: C 481 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7091 (mm-30) REVERT: D 619 LEU cc_start: 0.8391 (mt) cc_final: 0.8096 (tt) REVERT: D 653 GLN cc_start: 0.8744 (tp40) cc_final: 0.7885 (tm-30) REVERT: A 363 SER cc_start: 0.8412 (m) cc_final: 0.8109 (p) REVERT: A 432 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7465 (mtp-110) REVERT: B 588 ARG cc_start: 0.6992 (mmt180) cc_final: 0.6537 (mmt180) REVERT: B 612 SER cc_start: 0.6761 (m) cc_final: 0.6349 (t) REVERT: B 631 TRP cc_start: 0.7290 (t-100) cc_final: 0.7054 (t-100) REVERT: E 210 PHE cc_start: 0.7505 (m-80) cc_final: 0.7286 (m-80) REVERT: F 571 TRP cc_start: 0.8570 (t60) cc_final: 0.8285 (t60) REVERT: F 599 SER cc_start: 0.8865 (t) cc_final: 0.8591 (p) REVERT: F 626 MET cc_start: 0.6810 (mmp) cc_final: 0.6451 (mmt) REVERT: F 650 GLN cc_start: 0.8391 (tp40) cc_final: 0.8011 (tm-30) REVERT: F 651 ASN cc_start: 0.6902 (m-40) cc_final: 0.6490 (t0) outliers start: 4 outliers final: 1 residues processed: 358 average time/residue: 0.1345 time to fit residues: 68.5374 Evaluate side-chains 167 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 611 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 GLN D 630 GLN A 240 ASN A 425 ASN B 570 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.113747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093832 restraints weight = 35162.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.096043 restraints weight = 25095.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.097617 restraints weight = 16804.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.098872 restraints weight = 13848.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099216 restraints weight = 12038.436| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15150 Z= 0.164 Angle : 0.755 11.353 20754 Z= 0.368 Chirality : 0.049 0.441 2548 Planarity : 0.004 0.055 2546 Dihedral : 7.892 72.359 3187 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.44 % Allowed : 6.87 % Favored : 91.68 % 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: 0.91 (0.21), residues: 1591 helix: 1.90 (0.28), residues: 339 sheet: 0.54 (0.23), residues: 444 loop : 0.18 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 166 TYR 0.023 0.002 TYR D 643 PHE 0.017 0.002 PHE A 53 TRP 0.022 0.002 TRP C 478 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00361 (15056) covalent geometry : angle 0.69924 (20506) SS BOND : bond 0.00230 ( 34) SS BOND : angle 1.04007 ( 68) hydrogen bonds : bond 0.04994 ( 448) hydrogen bonds : angle 5.44501 ( 1215) link_BETA1-4 : bond 0.00926 ( 13) link_BETA1-4 : angle 3.29665 ( 39) link_NAG-ASN : bond 0.00773 ( 47) link_NAG-ASN : angle 3.03686 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 THR cc_start: 0.9017 (m) cc_final: 0.8658 (p) REVERT: C 195 ASN cc_start: 0.8415 (m-40) cc_final: 0.7991 (m-40) REVERT: C 432 ARG cc_start: 0.7057 (pmt-80) cc_final: 0.6728 (ppt170) REVERT: C 481 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6810 (mm-30) REVERT: D 619 LEU cc_start: 0.8251 (mt) cc_final: 0.7958 (tt) REVERT: D 653 GLN cc_start: 0.8465 (tp40) cc_final: 0.7475 (tm-30) REVERT: A 34 LEU cc_start: 0.3985 (mt) cc_final: 0.3626 (tt) REVERT: A 363 SER cc_start: 0.8446 (m) cc_final: 0.8140 (p) REVERT: A 390 PHE cc_start: 0.8685 (m-80) cc_final: 0.8485 (m-10) REVERT: A 432 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7264 (ppt170) REVERT: B 612 SER cc_start: 0.6403 (m) cc_final: 0.6007 (t) REVERT: B 626 MET cc_start: 0.6686 (tpp) cc_final: 0.6217 (tpp) REVERT: E 39 TYR cc_start: 0.8155 (m-80) cc_final: 0.7764 (m-80) REVERT: F 571 TRP cc_start: 0.8237 (t60) cc_final: 0.7893 (t60) REVERT: F 584 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7229 (tm-30) REVERT: F 626 MET cc_start: 0.6514 (mmp) cc_final: 0.6218 (mmm) REVERT: F 653 GLN cc_start: 0.8132 (mt0) cc_final: 0.7716 (tm-30) outliers start: 21 outliers final: 11 residues processed: 228 average time/residue: 0.1189 time to fit residues: 40.5836 Evaluate side-chains 172 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 617 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 138 optimal weight: 0.0470 chunk 56 optimal weight: 10.0000 chunk 33 optimal weight: 0.0980 chunk 150 optimal weight: 0.0010 chunk 6 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 656 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.112002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.092308 restraints weight = 36161.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.094652 restraints weight = 24237.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096572 restraints weight = 16388.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.097198 restraints weight = 12687.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.097703 restraints weight = 12247.184| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15150 Z= 0.152 Angle : 0.652 10.567 20754 Z= 0.319 Chirality : 0.046 0.425 2548 Planarity : 0.004 0.053 2546 Dihedral : 6.302 59.632 3187 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.99 % Allowed : 9.21 % Favored : 88.80 % 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: 0.80 (0.21), residues: 1591 helix: 2.14 (0.29), residues: 340 sheet: 0.35 (0.23), residues: 456 loop : 0.03 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.014 0.002 TYR D 638 PHE 0.024 0.002 PHE E 316 TRP 0.018 0.001 TRP B 614 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00340 (15056) covalent geometry : angle 0.61002 (20506) SS BOND : bond 0.00441 ( 34) SS BOND : angle 0.76458 ( 68) hydrogen bonds : bond 0.04277 ( 448) hydrogen bonds : angle 4.98547 ( 1215) link_BETA1-4 : bond 0.00826 ( 13) link_BETA1-4 : angle 2.46892 ( 39) link_NAG-ASN : bond 0.00507 ( 47) link_NAG-ASN : angle 2.54761 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 ASN cc_start: 0.8477 (m-40) cc_final: 0.8089 (m-40) REVERT: C 217 TYR cc_start: 0.8446 (m-80) cc_final: 0.8011 (m-80) REVERT: C 432 ARG cc_start: 0.7082 (pmt-80) cc_final: 0.6714 (ppt170) REVERT: C 481 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6804 (mm-30) REVERT: D 584 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7140 (mt-10) REVERT: D 619 LEU cc_start: 0.8402 (mt) cc_final: 0.8151 (tt) REVERT: D 629 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.7874 (mm) REVERT: D 653 GLN cc_start: 0.8487 (tp40) cc_final: 0.7359 (tm-30) REVERT: A 34 LEU cc_start: 0.4171 (mt) cc_final: 0.3886 (tt) REVERT: A 37 THR cc_start: 0.8956 (m) cc_final: 0.8651 (p) REVERT: A 363 SER cc_start: 0.8613 (m) cc_final: 0.8305 (p) REVERT: A 432 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7180 (ptt90) REVERT: B 571 TRP cc_start: 0.8314 (t60) cc_final: 0.8005 (t60) REVERT: B 626 MET cc_start: 0.6539 (tpp) cc_final: 0.6257 (tpp) REVERT: B 631 TRP cc_start: 0.7350 (t-100) cc_final: 0.7061 (t-100) REVERT: E 39 TYR cc_start: 0.8126 (m-80) cc_final: 0.7748 (m-80) REVERT: F 571 TRP cc_start: 0.8258 (t60) cc_final: 0.7947 (t60) REVERT: F 584 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7191 (tm-30) REVERT: F 619 LEU cc_start: 0.6965 (mp) cc_final: 0.6356 (tp) REVERT: F 626 MET cc_start: 0.6306 (mmp) cc_final: 0.5875 (mmm) REVERT: F 653 GLN cc_start: 0.8226 (mt0) cc_final: 0.7853 (tm-30) outliers start: 29 outliers final: 20 residues processed: 196 average time/residue: 0.1212 time to fit residues: 34.8331 Evaluate side-chains 167 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 617 LYS Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 4 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 116 optimal weight: 7.9990 chunk 69 optimal weight: 0.3980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 630 GLN E 99 ASN F 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.107875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088589 restraints weight = 36084.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090484 restraints weight = 25596.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.091807 restraints weight = 17808.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.092856 restraints weight = 14768.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093127 restraints weight = 13313.860| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15150 Z= 0.195 Angle : 0.672 10.599 20754 Z= 0.330 Chirality : 0.047 0.450 2548 Planarity : 0.004 0.050 2546 Dihedral : 5.614 58.336 3187 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.34 % Allowed : 9.35 % Favored : 88.32 % 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: 0.44 (0.21), residues: 1591 helix: 1.90 (0.29), residues: 347 sheet: -0.04 (0.23), residues: 459 loop : -0.13 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 542 TYR 0.013 0.002 TYR D 638 PHE 0.016 0.002 PHE E 360 TRP 0.031 0.002 TRP B 614 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00445 (15056) covalent geometry : angle 0.63591 (20506) SS BOND : bond 0.00324 ( 34) SS BOND : angle 0.85731 ( 68) hydrogen bonds : bond 0.04135 ( 448) hydrogen bonds : angle 4.82570 ( 1215) link_BETA1-4 : bond 0.00507 ( 13) link_BETA1-4 : angle 2.03970 ( 39) link_NAG-ASN : bond 0.00378 ( 47) link_NAG-ASN : angle 2.46417 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 ASN cc_start: 0.8451 (m-40) cc_final: 0.8152 (m-40) REVERT: C 217 TYR cc_start: 0.8617 (m-80) cc_final: 0.8148 (m-80) REVERT: C 432 ARG cc_start: 0.7262 (pmt-80) cc_final: 0.6955 (ppt170) REVERT: C 481 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6810 (mm-30) REVERT: D 523 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6994 (tp) REVERT: D 535 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.5584 (tmm) REVERT: D 584 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7140 (mt-10) REVERT: D 629 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8094 (mm) REVERT: D 630 GLN cc_start: 0.7643 (tt0) cc_final: 0.7143 (tt0) REVERT: A 37 THR cc_start: 0.9047 (m) cc_final: 0.8667 (p) REVERT: A 432 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7421 (ppt170) REVERT: B 626 MET cc_start: 0.6855 (tpp) cc_final: 0.5969 (tpp) REVERT: B 631 TRP cc_start: 0.7330 (t-100) cc_final: 0.6836 (t-100) REVERT: F 571 TRP cc_start: 0.8317 (t60) cc_final: 0.8056 (t60) REVERT: F 584 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7223 (tm-30) REVERT: F 628 TRP cc_start: 0.6603 (m100) cc_final: 0.5658 (m100) REVERT: F 653 GLN cc_start: 0.8279 (mt0) cc_final: 0.7924 (tm-30) outliers start: 34 outliers final: 21 residues processed: 180 average time/residue: 0.1201 time to fit residues: 32.0091 Evaluate side-chains 157 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 617 LYS Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 660 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 153 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 84 optimal weight: 0.0970 chunk 143 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 660 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 = 0.3669 r_free = 0.3669 target = 0.110036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090955 restraints weight = 35969.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092766 restraints weight = 26968.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094111 restraints weight = 18836.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.095784 restraints weight = 14735.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.096051 restraints weight = 12795.075| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15150 Z= 0.115 Angle : 0.595 10.369 20754 Z= 0.290 Chirality : 0.045 0.416 2548 Planarity : 0.003 0.049 2546 Dihedral : 5.221 59.302 3187 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.92 % Allowed : 9.76 % Favored : 88.32 % 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: 0.58 (0.21), residues: 1591 helix: 2.19 (0.29), residues: 341 sheet: 0.15 (0.23), residues: 446 loop : -0.19 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.019 0.001 TYR F 643 PHE 0.012 0.001 PHE C 53 TRP 0.017 0.001 TRP E 35 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00255 (15056) covalent geometry : angle 0.56083 (20506) SS BOND : bond 0.00190 ( 34) SS BOND : angle 0.58795 ( 68) hydrogen bonds : bond 0.03637 ( 448) hydrogen bonds : angle 4.57711 ( 1215) link_BETA1-4 : bond 0.00611 ( 13) link_BETA1-4 : angle 1.76347 ( 39) link_NAG-ASN : bond 0.00395 ( 47) link_NAG-ASN : angle 2.30696 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 432 ARG cc_start: 0.7145 (pmt-80) cc_final: 0.6794 (ppt170) REVERT: D 584 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7148 (mt-10) REVERT: D 648 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7954 (mm-30) REVERT: A 37 THR cc_start: 0.9043 (m) cc_final: 0.8754 (p) REVERT: A 432 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7388 (ppt170) REVERT: B 530 MET cc_start: 0.5923 (mtt) cc_final: 0.5354 (mtt) REVERT: B 626 MET cc_start: 0.6583 (tpp) cc_final: 0.5826 (tpp) REVERT: B 631 TRP cc_start: 0.7579 (t-100) cc_final: 0.7216 (t-100) REVERT: E 474 MET cc_start: 0.8244 (tpp) cc_final: 0.7888 (tpp) REVERT: F 584 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7221 (tm-30) REVERT: F 628 TRP cc_start: 0.6506 (m100) cc_final: 0.6163 (m100) REVERT: F 649 SER cc_start: 0.8382 (t) cc_final: 0.8175 (m) REVERT: F 653 GLN cc_start: 0.8170 (mt0) cc_final: 0.7888 (tm-30) outliers start: 28 outliers final: 20 residues processed: 175 average time/residue: 0.1217 time to fit residues: 31.4564 Evaluate side-chains 157 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 617 LYS Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.0040 chunk 2 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 121 optimal weight: 0.1980 chunk 133 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.110133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.090885 restraints weight = 35757.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.092871 restraints weight = 26670.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094244 restraints weight = 18792.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.095419 restraints weight = 14915.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.095946 restraints weight = 13358.954| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15150 Z= 0.112 Angle : 0.574 10.194 20754 Z= 0.280 Chirality : 0.044 0.421 2548 Planarity : 0.003 0.053 2546 Dihedral : 5.115 57.996 3187 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.99 % Allowed : 10.03 % Favored : 87.97 % 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: 0.69 (0.22), residues: 1591 helix: 2.26 (0.29), residues: 341 sheet: 0.19 (0.24), residues: 454 loop : -0.10 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 542 TYR 0.026 0.001 TYR F 643 PHE 0.011 0.001 PHE C 53 TRP 0.016 0.001 TRP B 614 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00248 (15056) covalent geometry : angle 0.54216 (20506) SS BOND : bond 0.00357 ( 34) SS BOND : angle 0.59425 ( 68) hydrogen bonds : bond 0.03475 ( 448) hydrogen bonds : angle 4.42696 ( 1215) link_BETA1-4 : bond 0.00638 ( 13) link_BETA1-4 : angle 1.67326 ( 39) link_NAG-ASN : bond 0.00374 ( 47) link_NAG-ASN : angle 2.19312 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 195 ASN cc_start: 0.8337 (m-40) cc_final: 0.7852 (m-40) REVERT: C 432 ARG cc_start: 0.7173 (pmt-80) cc_final: 0.6900 (ppt170) REVERT: D 523 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6878 (tp) REVERT: D 535 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.5683 (tmm) REVERT: D 584 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7159 (mt-10) REVERT: D 653 GLN cc_start: 0.8457 (tp40) cc_final: 0.7493 (tm-30) REVERT: D 655 LYS cc_start: 0.8906 (ttpp) cc_final: 0.8276 (mmtm) REVERT: A 432 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7112 (ppt170) REVERT: B 530 MET cc_start: 0.6088 (mtt) cc_final: 0.5359 (mtt) REVERT: B 626 MET cc_start: 0.6886 (tpp) cc_final: 0.6424 (tpp) REVERT: B 631 TRP cc_start: 0.7988 (t-100) cc_final: 0.7509 (t-100) REVERT: E 474 MET cc_start: 0.8295 (tpp) cc_final: 0.8045 (tpp) REVERT: F 584 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7229 (tm-30) REVERT: F 628 TRP cc_start: 0.6530 (m100) cc_final: 0.6235 (m100) REVERT: F 653 GLN cc_start: 0.8155 (mt0) cc_final: 0.7877 (tm-30) outliers start: 29 outliers final: 19 residues processed: 172 average time/residue: 0.1350 time to fit residues: 34.1644 Evaluate side-chains 158 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 617 LYS Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 660 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.105108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085701 restraints weight = 36418.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087229 restraints weight = 27463.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088371 restraints weight = 20061.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.089735 restraints weight = 16946.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089994 restraints weight = 15115.876| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 15150 Z= 0.271 Angle : 0.732 10.925 20754 Z= 0.358 Chirality : 0.049 0.495 2548 Planarity : 0.004 0.059 2546 Dihedral : 5.861 55.471 3187 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.41 % Allowed : 10.86 % Favored : 86.74 % 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: 0.20 (0.21), residues: 1591 helix: 1.85 (0.29), residues: 341 sheet: -0.28 (0.23), residues: 460 loop : -0.28 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 503 TYR 0.022 0.002 TYR C 39 PHE 0.024 0.003 PHE E 360 TRP 0.029 0.002 TRP B 614 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00631 (15056) covalent geometry : angle 0.70079 (20506) SS BOND : bond 0.00445 ( 34) SS BOND : angle 0.98592 ( 68) hydrogen bonds : bond 0.04241 ( 448) hydrogen bonds : angle 4.85284 ( 1215) link_BETA1-4 : bond 0.00446 ( 13) link_BETA1-4 : angle 1.96467 ( 39) link_NAG-ASN : bond 0.00367 ( 47) link_NAG-ASN : angle 2.44322 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 432 ARG cc_start: 0.7463 (pmt-80) cc_final: 0.7157 (ppt170) REVERT: D 523 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7044 (tp) REVERT: D 535 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6148 (tmm) REVERT: D 652 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 653 GLN cc_start: 0.8575 (tp40) cc_final: 0.7590 (tm-30) REVERT: A 104 MET cc_start: 0.9098 (ttt) cc_final: 0.8855 (ttt) REVERT: A 376 ASN cc_start: 0.8769 (t0) cc_final: 0.8466 (t0) REVERT: A 432 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7241 (ppt170) REVERT: B 626 MET cc_start: 0.7289 (tpp) cc_final: 0.6898 (tpp) REVERT: E 474 MET cc_start: 0.8350 (tpp) cc_final: 0.7947 (tpp) REVERT: F 584 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7153 (tm-30) REVERT: F 610 TRP cc_start: 0.2952 (t-100) cc_final: 0.2583 (t-100) REVERT: F 653 GLN cc_start: 0.8404 (mt0) cc_final: 0.7979 (tm-30) outliers start: 35 outliers final: 28 residues processed: 173 average time/residue: 0.1350 time to fit residues: 34.2400 Evaluate side-chains 161 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 617 LYS Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 660 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 103 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 82 optimal weight: 0.0870 chunk 85 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.107770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088921 restraints weight = 36022.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.090392 restraints weight = 28697.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.091720 restraints weight = 20506.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093086 restraints weight = 16076.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093374 restraints weight = 14391.724| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15150 Z= 0.124 Angle : 0.615 13.529 20754 Z= 0.297 Chirality : 0.045 0.431 2548 Planarity : 0.004 0.059 2546 Dihedral : 5.481 57.870 3187 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.44 % Allowed : 12.58 % Favored : 85.98 % 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: 1591 helix: 2.01 (0.29), residues: 341 sheet: -0.20 (0.23), residues: 454 loop : -0.25 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 542 TYR 0.013 0.001 TYR C 39 PHE 0.012 0.001 PHE C 53 TRP 0.027 0.001 TRP B 614 HIS 0.003 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00283 (15056) covalent geometry : angle 0.58364 (20506) SS BOND : bond 0.00237 ( 34) SS BOND : angle 0.64837 ( 68) hydrogen bonds : bond 0.03610 ( 448) hydrogen bonds : angle 4.59412 ( 1215) link_BETA1-4 : bond 0.00553 ( 13) link_BETA1-4 : angle 1.67315 ( 39) link_NAG-ASN : bond 0.00357 ( 47) link_NAG-ASN : angle 2.26343 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 432 ARG cc_start: 0.7296 (pmt-80) cc_final: 0.6988 (ppt170) REVERT: D 653 GLN cc_start: 0.8520 (tp40) cc_final: 0.7442 (tm-30) REVERT: D 655 LYS cc_start: 0.8935 (ttpp) cc_final: 0.8332 (mmtm) REVERT: A 99 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8077 (t0) REVERT: A 104 MET cc_start: 0.9067 (ttt) cc_final: 0.8840 (ttt) REVERT: A 376 ASN cc_start: 0.8850 (t0) cc_final: 0.8561 (t0) REVERT: A 432 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7107 (ppt170) REVERT: B 621 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7996 (tm-30) REVERT: B 626 MET cc_start: 0.7485 (tpp) cc_final: 0.6962 (tpp) REVERT: E 474 MET cc_start: 0.8282 (tpp) cc_final: 0.7885 (tpp) REVERT: F 584 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7226 (tm-30) REVERT: F 610 TRP cc_start: 0.2928 (t-100) cc_final: 0.2667 (t-100) REVERT: F 628 TRP cc_start: 0.6764 (m100) cc_final: 0.5830 (m100) REVERT: F 632 ASP cc_start: 0.8187 (t0) cc_final: 0.7705 (t0) REVERT: F 653 GLN cc_start: 0.8328 (mt0) cc_final: 0.7974 (tm-30) outliers start: 21 outliers final: 16 residues processed: 161 average time/residue: 0.1297 time to fit residues: 30.8836 Evaluate side-chains 149 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 617 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 660 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 143 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 0 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** 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 = 0.3586 r_free = 0.3586 target = 0.104731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085351 restraints weight = 36721.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086795 restraints weight = 27587.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087541 restraints weight = 20098.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088748 restraints weight = 17609.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.089152 restraints weight = 15823.890| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 15150 Z= 0.249 Angle : 0.724 13.489 20754 Z= 0.352 Chirality : 0.048 0.479 2548 Planarity : 0.004 0.060 2546 Dihedral : 5.971 57.661 3187 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.79 % Allowed : 13.13 % Favored : 85.09 % 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: 0.06 (0.21), residues: 1591 helix: 1.80 (0.29), residues: 341 sheet: -0.44 (0.23), residues: 462 loop : -0.36 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 542 TYR 0.023 0.002 TYR C 39 PHE 0.021 0.002 PHE E 360 TRP 0.031 0.002 TRP B 614 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00578 (15056) covalent geometry : angle 0.69267 (20506) SS BOND : bond 0.00387 ( 34) SS BOND : angle 0.94594 ( 68) hydrogen bonds : bond 0.04125 ( 448) hydrogen bonds : angle 4.88770 ( 1215) link_BETA1-4 : bond 0.00580 ( 13) link_BETA1-4 : angle 1.94376 ( 39) link_NAG-ASN : bond 0.00344 ( 47) link_NAG-ASN : angle 2.42277 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 432 ARG cc_start: 0.7436 (pmt-80) cc_final: 0.7227 (ppt170) REVERT: C 474 MET cc_start: 0.8782 (tmm) cc_final: 0.8248 (tmm) REVERT: D 535 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6385 (tmm) REVERT: D 652 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7655 (tm-30) REVERT: D 653 GLN cc_start: 0.8587 (tp40) cc_final: 0.7567 (tm-30) REVERT: A 376 ASN cc_start: 0.8829 (t0) cc_final: 0.8619 (t0) REVERT: A 432 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7251 (ppt170) REVERT: B 621 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7879 (tm-30) REVERT: B 626 MET cc_start: 0.7531 (tpp) cc_final: 0.7259 (tpp) REVERT: E 474 MET cc_start: 0.8307 (tpp) cc_final: 0.7951 (tpp) REVERT: F 584 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7184 (tm-30) REVERT: F 610 TRP cc_start: 0.3062 (t-100) cc_final: 0.2791 (t-100) REVERT: F 632 ASP cc_start: 0.8394 (t0) cc_final: 0.7747 (t0) REVERT: F 653 GLN cc_start: 0.8435 (mt0) cc_final: 0.7996 (tm-30) outliers start: 26 outliers final: 21 residues processed: 154 average time/residue: 0.1291 time to fit residues: 29.5798 Evaluate side-chains 150 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 617 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 660 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.106337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087311 restraints weight = 36326.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.089119 restraints weight = 26471.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.090167 restraints weight = 19141.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.091517 restraints weight = 15833.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.091835 restraints weight = 14009.278| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15150 Z= 0.156 Angle : 0.640 13.265 20754 Z= 0.311 Chirality : 0.046 0.441 2548 Planarity : 0.004 0.057 2546 Dihedral : 5.737 54.836 3187 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.37 % Allowed : 13.40 % Favored : 85.22 % 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 (0.22), residues: 1591 helix: 1.90 (0.29), residues: 341 sheet: -0.43 (0.23), residues: 466 loop : -0.33 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 542 TYR 0.016 0.001 TYR C 39 PHE 0.013 0.002 PHE C 53 TRP 0.024 0.001 TRP B 614 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00362 (15056) covalent geometry : angle 0.60784 (20506) SS BOND : bond 0.00270 ( 34) SS BOND : angle 0.71881 ( 68) hydrogen bonds : bond 0.03721 ( 448) hydrogen bonds : angle 4.71794 ( 1215) link_BETA1-4 : bond 0.00545 ( 13) link_BETA1-4 : angle 1.74159 ( 39) link_NAG-ASN : bond 0.00324 ( 47) link_NAG-ASN : angle 2.32004 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 474 MET cc_start: 0.8732 (tmm) cc_final: 0.8156 (tmm) REVERT: D 535 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6400 (tmm) REVERT: D 653 GLN cc_start: 0.8592 (tp40) cc_final: 0.7641 (tm-30) REVERT: D 655 LYS cc_start: 0.8922 (ttpp) cc_final: 0.8333 (mmtm) REVERT: A 104 MET cc_start: 0.8964 (ttt) cc_final: 0.8722 (ttt) REVERT: A 376 ASN cc_start: 0.8843 (t0) cc_final: 0.8642 (t0) REVERT: A 432 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7230 (ppt170) REVERT: B 621 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7970 (tp30) REVERT: B 626 MET cc_start: 0.7903 (tpp) cc_final: 0.7313 (tpp) REVERT: E 474 MET cc_start: 0.8279 (tpp) cc_final: 0.8009 (tpp) REVERT: F 584 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7241 (tm-30) REVERT: F 610 TRP cc_start: 0.3128 (t-100) cc_final: 0.2906 (t-100) REVERT: F 628 TRP cc_start: 0.6511 (m100) cc_final: 0.5423 (m100) REVERT: F 632 ASP cc_start: 0.8363 (t0) cc_final: 0.7819 (t0) REVERT: F 648 GLU cc_start: 0.8173 (pp20) cc_final: 0.7751 (pp20) REVERT: F 653 GLN cc_start: 0.8360 (mt0) cc_final: 0.7953 (tm-30) outliers start: 20 outliers final: 19 residues processed: 149 average time/residue: 0.1256 time to fit residues: 28.2799 Evaluate side-chains 145 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 617 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 660 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 79 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 63 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 652 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.108174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.089044 restraints weight = 35709.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.090689 restraints weight = 26369.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.091938 restraints weight = 19051.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093212 restraints weight = 15679.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093502 restraints weight = 14147.590| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15150 Z= 0.118 Angle : 0.614 13.495 20754 Z= 0.299 Chirality : 0.045 0.419 2548 Planarity : 0.004 0.059 2546 Dihedral : 5.448 59.217 3187 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.37 % Allowed : 13.75 % Favored : 84.88 % 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: 0.24 (0.22), residues: 1591 helix: 2.04 (0.29), residues: 340 sheet: -0.34 (0.24), residues: 456 loop : -0.28 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 542 TYR 0.013 0.001 TYR C 39 PHE 0.012 0.001 PHE C 53 TRP 0.027 0.001 TRP B 631 HIS 0.003 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00270 (15056) covalent geometry : angle 0.58462 (20506) SS BOND : bond 0.00190 ( 34) SS BOND : angle 0.59117 ( 68) hydrogen bonds : bond 0.03424 ( 448) hydrogen bonds : angle 4.53561 ( 1215) link_BETA1-4 : bond 0.00595 ( 13) link_BETA1-4 : angle 1.66584 ( 39) link_NAG-ASN : bond 0.00351 ( 47) link_NAG-ASN : angle 2.21727 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2202.95 seconds wall clock time: 39 minutes 7.94 seconds (2347.94 seconds total)