Starting phenix.real_space_refine on Thu Sep 18 07:39:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nhm_49416/09_2025/9nhm_49416.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nhm_49416/09_2025/9nhm_49416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nhm_49416/09_2025/9nhm_49416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nhm_49416/09_2025/9nhm_49416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nhm_49416/09_2025/9nhm_49416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nhm_49416/09_2025/9nhm_49416.map" } resolution = 4.0 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 103 5.16 5 C 9287 2.51 5 N 2504 2.21 5 O 3003 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 14897 Number of models: 1 Model: "" Number of chains: 20 Chain: "H" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 629 Classifications: {'peptide': 122} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 117} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "L" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 527 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'UNK:plan-1': 98} Unresolved non-hydrogen planarities: 98 Chain: "C" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3368 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 3 Chain: "D" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 851 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain breaks: 1 Chain: "A" 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: "B" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 865 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain breaks: 1 Chain: "E" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3373 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 22, 'TRANS': 408} Chain breaks: 3 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 990 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 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: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 4.00, per 1000 atoms: 0.27 Number of scatterers: 14897 At special positions: 0 Unit cell: (121.9, 131.1, 131.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 103 16.00 O 3003 8.00 N 2504 7.00 C 9287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.08 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 378 " - pdb=" SG CYS C 446 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 419 " distance=2.06 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS B 663 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 663 " - pdb=" SG CYS E 501 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 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=2.08 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 446 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS F 663 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.07 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.04 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 378 " - pdb=" SG CYS E 446 " distance=2.07 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 419 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 197 " " NAG A 605 " - " ASN A 230 " " NAG A 606 " - " ASN A 289 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 332 " " NAG A 609 " - " ASN A 386 " " NAG A 610 " - " ASN A 443 " " NAG A 611 " - " ASN A 449 " " NAG A 612 " - " ASN A 88 " " NAG A 613 " - " ASN A 357 " " NAG B 701 " - " ASN B 656 " " 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 386 " " NAG C 607 " - " ASN C 443 " " NAG C 608 " - " ASN C 449 " " NAG C 609 " - " ASN C 133 " " NAG C 610 " - " ASN C 392 " " NAG C 611 " - " ASN C 357 " " NAG C 612 " - " ASN C 156 " " NAG C 613 " - " ASN C 332 " " NAG C 614 " - " ASN C 339 " " NAG C 615 " - " ASN C 276 " " NAG D 701 " - " ASN D 656 " " NAG D 702 " - " ASN D 611 " " NAG D 703 " - " ASN D 637 " " NAG D 704 " - " ASN D 616 " " NAG E 601 " - " ASN E 130 " " NAG E 602 " - " ASN E 156 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 230 " " NAG E 606 " - " ASN E 289 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 332 " " NAG E 609 " - " ASN E 443 " " NAG E 610 " - " ASN E 449 " " NAG E 611 " - " ASN E 88 " " NAG E 612 " - " ASN E 133 " " NAG E 613 " - " ASN E 386 " " NAG E 614 " - " ASN E 357 " " NAG G 1 " - " ASN C 241 " " NAG I 1 " - " ASN C 262 " " NAG J 1 " - " ASN C 301 " " 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: 1.49 Conformation dependent library (CDL) restraints added in 713.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3498 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 26 sheets defined 26.4% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... 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 'C' and resid 67 through 73 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.104A 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 368 through 373 Processing helix chain 'C' and resid 476 through 484 removed outlier: 5.178A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 574 through 595 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 624 through 626 No H-bonds generated for 'chain 'D' and resid 624 through 626' Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 658 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.141A 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 195 through 198 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.072A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 426 through 430 removed outlier: 4.128A pdb=" N GLU A 430 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.767A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.900A pdb=" N SER B 534 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 596 Processing helix chain 'B' and resid 620 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 476 through 481 Processing helix chain 'F' and resid 521 through 528 removed outlier: 4.291A pdb=" N ALA F 525 " --> pdb=" O PHE F 522 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.519A pdb=" N LYS F 574 " --> pdb=" O HIS F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 removed outlier: 4.033A pdb=" N CYS H 22 " --> pdb=" O UNK H 77 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N UNK H 77 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 55 through 58 removed outlier: 6.042A pdb=" N UNK H 55 " --> pdb=" O UNK H 51 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N UNK H 51 " --> pdb=" O UNK H 55 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N UNK H 46 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N UNK H 37 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N UNK H 50 " --> pdb=" O UNK H 33 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N UNK H 33 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N UNK H 32 " --> pdb=" O UNK H 97 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N UNK H 97 " --> pdb=" O UNK H 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.816A pdb=" N TRP L 36 " --> pdb=" O UNK L 48 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N UNK L 84 " --> pdb=" O UNK L 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.313A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA7, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AA8, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA9, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.434A pdb=" N ALA C 200 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N TYR C 436 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 202 " --> pdb=" O TYR C 436 " (cutoff:3.500A) Processing sheet with id=AB1, 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 284 through 302 removed outlier: 7.601A pdb=" N LYS C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.581A 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 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 382 through 385 current: chain 'C' and resid 467 through 469 Processing sheet with id=AB2, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.425A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AB4, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'A' and resid 53 through 56 removed outlier: 4.768A pdb=" N ALA A 55 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N HIS A 216 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AB7, first strand: chain 'A' and resid 170 through 177 removed outlier: 5.950A pdb=" N MET A 154 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.664A pdb=" N THR A 202 " --> pdb=" O TYR A 436 " (cutoff:3.500A) Processing sheet with id=AB9, 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 312 removed outlier: 5.461A pdb=" N THR A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR A 320 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 324 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.221A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.873A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.355A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AC6, first strand: chain 'E' and resid 181 through 185 removed outlier: 7.366A pdb=" N GLN E 190 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.334A pdb=" N THR E 202 " --> pdb=" O TYR E 436 " (cutoff:3.500A) Processing sheet with id=AC8, 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 312 removed outlier: 5.397A pdb=" N THR E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N THR E 320 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 324 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 467 through 469 442 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.90 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: 4063 1.33 - 1.48: 4605 1.48 - 1.62: 6357 1.62 - 1.77: 36 1.77 - 1.92: 104 Bond restraints: 15165 Sorted by residual: bond pdb=" CB LEU B 523 " pdb=" CG LEU B 523 " ideal model delta sigma weight residual 1.530 1.671 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" CZ2 TRP A 395 " pdb=" CH2 TRP A 395 " ideal model delta sigma weight residual 1.368 1.494 -0.126 1.90e-02 2.77e+03 4.40e+01 bond pdb=" CB ILE B 573 " pdb=" CG1 ILE B 573 " ideal model delta sigma weight residual 1.530 1.658 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" CD2 TRP A 395 " pdb=" CE3 TRP A 395 " ideal model delta sigma weight residual 1.398 1.498 -0.100 1.60e-02 3.91e+03 3.91e+01 bond pdb=" CB LEU F 520 " pdb=" CG LEU F 520 " ideal model delta sigma weight residual 1.530 1.655 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 15160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 18080 2.49 - 4.99: 2263 4.99 - 7.48: 272 7.48 - 9.97: 32 9.97 - 12.46: 2 Bond angle restraints: 20649 Sorted by residual: angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 128.25 -8.69 1.02e+00 9.61e-01 7.25e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 128.01 -8.45 1.02e+00 9.61e-01 6.87e+01 angle pdb=" N PRO E 438 " pdb=" CA PRO E 438 " pdb=" C PRO E 438 " ideal model delta sigma weight residual 110.47 102.78 7.69 9.60e-01 1.09e+00 6.41e+01 angle pdb=" C ALA A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta sigma weight residual 120.03 127.75 -7.72 9.90e-01 1.02e+00 6.08e+01 angle pdb=" C CYS A 205 " pdb=" N PRO A 206 " pdb=" CA PRO A 206 " ideal model delta sigma weight residual 119.56 127.11 -7.55 1.02e+00 9.61e-01 5.47e+01 ... (remaining 20644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 9715 24.59 - 49.17: 179 49.17 - 73.76: 57 73.76 - 98.35: 24 98.35 - 122.93: 13 Dihedral angle restraints: 9988 sinusoidal: 4612 harmonic: 5376 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 157.35 -64.35 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS B 663 " pdb=" CB CYS B 663 " ideal model delta sinusoidal sigma weight residual 93.00 138.22 -45.22 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CB CYS D 663 " pdb=" SG CYS D 663 " pdb=" SG CYS E 501 " pdb=" CB CYS E 501 " ideal model delta sinusoidal sigma weight residual 93.00 137.93 -44.93 1 1.00e+01 1.00e-02 2.80e+01 ... (remaining 9985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1918 0.122 - 0.244: 393 0.244 - 0.366: 173 0.366 - 0.487: 95 0.487 - 0.609: 6 Chirality restraints: 2585 Sorted by residual: 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 -2.65 0.25 2.00e-02 2.50e+03 1.53e+02 chirality pdb=" C1 NAG G 3 " pdb=" O4 NAG G 2 " pdb=" C2 NAG G 3 " pdb=" O5 NAG G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.51e+02 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 -2.64 0.24 2.00e-02 2.50e+03 1.45e+02 ... (remaining 2582 not shown) Planarity restraints: 2612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 611 " -0.266 2.00e-02 2.50e+03 2.21e-01 6.09e+02 pdb=" C7 NAG E 611 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG E 611 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG E 611 " 0.367 2.00e-02 2.50e+03 pdb=" O7 NAG E 611 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 197 " 0.089 2.00e-02 2.50e+03 9.39e-02 1.10e+02 pdb=" CG ASN A 197 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 197 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 197 " -0.146 2.00e-02 2.50e+03 pdb=" C1 NAG A 604 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 230 " -0.080 2.00e-02 2.50e+03 8.28e-02 8.58e+01 pdb=" CG ASN E 230 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 230 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN E 230 " 0.126 2.00e-02 2.50e+03 pdb=" C1 NAG E 605 " -0.102 2.00e-02 2.50e+03 ... (remaining 2609 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1936 2.74 - 3.28: 14308 3.28 - 3.82: 23788 3.82 - 4.36: 29873 4.36 - 4.90: 47006 Nonbonded interactions: 116911 Sorted by model distance: nonbonded pdb=" OG1 THR E 373 " pdb=" O CYS E 385 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR A 373 " pdb=" O CYS A 385 " model vdw 2.242 3.040 nonbonded pdb=" N ASP C 474 " pdb=" OD1 ASP C 474 " model vdw 2.398 3.120 nonbonded pdb=" N ASN C 478 " pdb=" OD1 ASN C 478 " model vdw 2.400 3.120 ... (remaining 116906 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 458 or resid 466 through 505 or resid 601 throu \ gh 613)) selection = (chain 'C' and (resid 35 through 505 or resid 602 through 614)) selection = (chain 'E' and (resid 35 through 458 or resid 466 through 505 or resid 601 throu \ gh 613)) } ncs_group { reference = (chain 'B' and (resid 523 through 535 or resid 573 through 664)) selection = (chain 'D' and resid 523 through 664) selection = (chain 'F' and (resid 523 through 535 or resid 573 through 664)) } 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: 5.220 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.810 Find NCS groups from input model: 0.350 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 0.141 15267 Z= 1.129 Angle : 1.726 12.463 20920 Z= 1.094 Chirality : 0.141 0.609 2585 Planarity : 0.010 0.221 2558 Dihedral : 11.904 122.935 6385 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.20), residues: 1596 helix: 0.09 (0.25), residues: 364 sheet: 0.67 (0.25), residues: 380 loop : 0.21 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 298 TYR 0.047 0.008 TYR E 40 PHE 0.033 0.006 PHE A 317 TRP 0.061 0.010 TRP E 35 HIS 0.008 0.002 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.02081 (15165) covalent geometry : angle 1.69572 (20649) SS BOND : bond 0.01714 ( 35) SS BOND : angle 3.30035 ( 70) hydrogen bonds : bond 0.14822 ( 442) hydrogen bonds : angle 7.49239 ( 1191) link_BETA1-4 : bond 0.07362 ( 13) link_BETA1-4 : angle 5.05383 ( 39) link_NAG-ASN : bond 0.08160 ( 54) link_NAG-ASN : angle 2.73614 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 VAL cc_start: 0.9661 (t) cc_final: 0.9403 (p) REVERT: C 51 THR cc_start: 0.9359 (m) cc_final: 0.9132 (p) REVERT: C 80 ASN cc_start: 0.8494 (m-40) cc_final: 0.8280 (m110) REVERT: C 317 PHE cc_start: 0.8474 (t80) cc_final: 0.8212 (t80) REVERT: C 478 ASN cc_start: 0.8086 (p0) cc_final: 0.7370 (p0) REVERT: D 579 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8381 (mtt180) REVERT: D 591 GLN cc_start: 0.9335 (tt0) cc_final: 0.9135 (tt0) REVERT: D 639 THR cc_start: 0.9180 (m) cc_final: 0.8877 (p) REVERT: A 84 ILE cc_start: 0.8575 (mt) cc_final: 0.8201 (mm) REVERT: A 107 ASP cc_start: 0.8858 (m-30) cc_final: 0.8579 (t0) REVERT: A 120 VAL cc_start: 0.9232 (t) cc_final: 0.9012 (t) REVERT: B 654 GLU cc_start: 0.8641 (tp30) cc_final: 0.8294 (tp30) REVERT: E 52 LEU cc_start: 0.8827 (mt) cc_final: 0.8432 (mm) REVERT: E 80 ASN cc_start: 0.8524 (t0) cc_final: 0.7993 (p0) REVERT: F 522 PHE cc_start: 0.7766 (t80) cc_final: 0.7485 (t80) REVERT: F 653 GLN cc_start: 0.9084 (tt0) cc_final: 0.8691 (tt0) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1393 time to fit residues: 59.9031 Evaluate side-chains 133 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 ASN C 229 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN A 355 HIS E 72 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.080496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.067886 restraints weight = 59179.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.069846 restraints weight = 33440.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.071199 restraints weight = 22515.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.072141 restraints weight = 16901.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.072680 restraints weight = 13674.764| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15267 Z= 0.171 Angle : 0.767 11.936 20920 Z= 0.380 Chirality : 0.047 0.248 2585 Planarity : 0.004 0.042 2558 Dihedral : 8.305 96.592 3337 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.96 % Allowed : 7.34 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.21), residues: 1596 helix: 1.23 (0.26), residues: 364 sheet: 0.21 (0.24), residues: 411 loop : 0.05 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 327 TYR 0.034 0.002 TYR F 643 PHE 0.018 0.002 PHE C 53 TRP 0.031 0.002 TRP A 479 HIS 0.007 0.001 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00383 (15165) covalent geometry : angle 0.72281 (20649) SS BOND : bond 0.00215 ( 35) SS BOND : angle 1.43022 ( 70) hydrogen bonds : bond 0.05263 ( 442) hydrogen bonds : angle 5.55729 ( 1191) link_BETA1-4 : bond 0.00852 ( 13) link_BETA1-4 : angle 3.46025 ( 39) link_NAG-ASN : bond 0.00531 ( 54) link_NAG-ASN : angle 2.37037 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 VAL cc_start: 0.9469 (t) cc_final: 0.9039 (p) REVERT: C 51 THR cc_start: 0.9261 (m) cc_final: 0.8953 (p) REVERT: C 80 ASN cc_start: 0.8435 (m-40) cc_final: 0.8220 (m110) REVERT: C 475 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.4420 (ppp) REVERT: C 478 ASN cc_start: 0.8009 (p0) cc_final: 0.7149 (p0) REVERT: C 479 TRP cc_start: 0.8466 (m-10) cc_final: 0.7233 (m-90) REVERT: D 584 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8203 (tm-30) REVERT: D 589 ASP cc_start: 0.8640 (m-30) cc_final: 0.8257 (t0) REVERT: D 650 GLN cc_start: 0.8899 (tt0) cc_final: 0.8697 (tt0) REVERT: A 84 ILE cc_start: 0.8369 (mt) cc_final: 0.8105 (mm) REVERT: B 530 MET cc_start: 0.6130 (mtm) cc_final: 0.5754 (ttm) REVERT: B 577 GLN cc_start: 0.8678 (tp40) cc_final: 0.8331 (tp40) REVERT: B 628 TRP cc_start: 0.8083 (m100) cc_final: 0.7788 (m100) REVERT: B 635 ILE cc_start: 0.8776 (pt) cc_final: 0.8555 (tt) REVERT: B 642 ILE cc_start: 0.9286 (mt) cc_final: 0.8734 (tt) REVERT: B 647 GLU cc_start: 0.8418 (pp20) cc_final: 0.8213 (pp20) REVERT: B 661 LEU cc_start: 0.6215 (tp) cc_final: 0.5647 (pt) REVERT: E 80 ASN cc_start: 0.8896 (t0) cc_final: 0.8098 (p0) REVERT: E 195 ASN cc_start: 0.8239 (t0) cc_final: 0.7857 (t0) outliers start: 14 outliers final: 4 residues processed: 177 average time/residue: 0.1187 time to fit residues: 31.7984 Evaluate side-chains 124 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain F residue 591 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 96 optimal weight: 8.9990 chunk 89 optimal weight: 0.4980 chunk 109 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 640 GLN D 651 ASN A 82 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.077962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065180 restraints weight = 59991.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.067077 restraints weight = 34330.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.068348 restraints weight = 23419.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.069195 restraints weight = 17908.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.069842 restraints weight = 14823.714| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15267 Z= 0.161 Angle : 0.678 10.814 20920 Z= 0.330 Chirality : 0.045 0.270 2585 Planarity : 0.003 0.030 2558 Dihedral : 6.714 91.106 3337 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.65 % Allowed : 7.34 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.47 (0.21), residues: 1596 helix: 1.67 (0.28), residues: 367 sheet: 0.14 (0.26), residues: 389 loop : -0.14 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 308 TYR 0.029 0.002 TYR F 643 PHE 0.013 0.002 PHE C 53 TRP 0.024 0.002 TRP D 623 HIS 0.004 0.001 HIS D 585 Details of bonding type rmsd covalent geometry : bond 0.00365 (15165) covalent geometry : angle 0.64730 (20649) SS BOND : bond 0.00250 ( 35) SS BOND : angle 1.12954 ( 70) hydrogen bonds : bond 0.04285 ( 442) hydrogen bonds : angle 5.22100 ( 1191) link_BETA1-4 : bond 0.00664 ( 13) link_BETA1-4 : angle 2.46449 ( 39) link_NAG-ASN : bond 0.00331 ( 54) link_NAG-ASN : angle 1.98869 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 THR cc_start: 0.9220 (m) cc_final: 0.8869 (p) REVERT: C 80 ASN cc_start: 0.8550 (m-40) cc_final: 0.8342 (m110) REVERT: C 317 PHE cc_start: 0.7938 (t80) cc_final: 0.7388 (t80) REVERT: C 475 MET cc_start: 0.7415 (ppp) cc_final: 0.5100 (ppp) REVERT: C 478 ASN cc_start: 0.8156 (p0) cc_final: 0.7177 (p0) REVERT: C 479 TRP cc_start: 0.8333 (m-10) cc_final: 0.7144 (m-90) REVERT: D 584 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8256 (tm-30) REVERT: D 589 ASP cc_start: 0.8701 (m-30) cc_final: 0.8267 (t0) REVERT: D 650 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8708 (tt0) REVERT: A 84 ILE cc_start: 0.8225 (mt) cc_final: 0.7780 (mm) REVERT: B 581 LEU cc_start: 0.9095 (tp) cc_final: 0.8761 (tp) REVERT: B 584 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 628 TRP cc_start: 0.8325 (m100) cc_final: 0.8117 (m100) REVERT: B 647 GLU cc_start: 0.8557 (pp20) cc_final: 0.8321 (pp20) REVERT: B 653 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8817 (tm-30) REVERT: B 654 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8231 (tp30) REVERT: B 661 LEU cc_start: 0.6432 (tp) cc_final: 0.5744 (pp) REVERT: E 80 ASN cc_start: 0.8913 (t0) cc_final: 0.8134 (p0) REVERT: E 95 MET cc_start: 0.8972 (ptm) cc_final: 0.8714 (mtm) REVERT: E 195 ASN cc_start: 0.8283 (t0) cc_final: 0.7847 (t0) REVERT: F 535 MET cc_start: 0.8695 (mmt) cc_final: 0.8396 (mmp) outliers start: 24 outliers final: 13 residues processed: 137 average time/residue: 0.1150 time to fit residues: 24.2484 Evaluate side-chains 119 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 591 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 33 optimal weight: 0.0770 chunk 108 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.077505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.064765 restraints weight = 60070.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.066656 restraints weight = 34356.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067955 restraints weight = 23342.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068845 restraints weight = 17743.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.069475 restraints weight = 14575.228| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15267 Z= 0.126 Angle : 0.605 10.847 20920 Z= 0.297 Chirality : 0.044 0.266 2585 Planarity : 0.003 0.029 2558 Dihedral : 5.749 84.260 3337 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.71 % Allowed : 7.61 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.21), residues: 1596 helix: 1.79 (0.29), residues: 361 sheet: 0.00 (0.25), residues: 397 loop : -0.11 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.014 0.001 TYR F 643 PHE 0.012 0.001 PHE C 53 TRP 0.027 0.002 TRP E 69 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00284 (15165) covalent geometry : angle 0.57635 (20649) SS BOND : bond 0.00265 ( 35) SS BOND : angle 0.93744 ( 70) hydrogen bonds : bond 0.03740 ( 442) hydrogen bonds : angle 4.92027 ( 1191) link_BETA1-4 : bond 0.00581 ( 13) link_BETA1-4 : angle 2.03585 ( 39) link_NAG-ASN : bond 0.00294 ( 54) link_NAG-ASN : angle 1.88269 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 THR cc_start: 0.9194 (m) cc_final: 0.8855 (p) REVERT: C 102 GLU cc_start: 0.8148 (mp0) cc_final: 0.7874 (mp0) REVERT: C 317 PHE cc_start: 0.7859 (t80) cc_final: 0.7463 (t80) REVERT: C 475 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.5041 (ppp) REVERT: C 478 ASN cc_start: 0.8147 (p0) cc_final: 0.7207 (p0) REVERT: C 479 TRP cc_start: 0.8294 (m-10) cc_final: 0.7149 (m-90) REVERT: D 584 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8260 (tm-30) REVERT: D 650 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8647 (tt0) REVERT: A 84 ILE cc_start: 0.8242 (mt) cc_final: 0.7839 (mm) REVERT: B 530 MET cc_start: 0.6559 (mtm) cc_final: 0.5712 (mtt) REVERT: B 577 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8156 (tm-30) REVERT: B 581 LEU cc_start: 0.9110 (tp) cc_final: 0.8747 (tp) REVERT: B 584 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 647 GLU cc_start: 0.8596 (pp20) cc_final: 0.8335 (pp20) REVERT: B 648 GLU cc_start: 0.8960 (tp30) cc_final: 0.8683 (tp30) REVERT: B 654 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8558 (tp30) REVERT: B 661 LEU cc_start: 0.6603 (tp) cc_final: 0.5901 (pp) REVERT: E 80 ASN cc_start: 0.8923 (t0) cc_final: 0.8099 (p0) REVERT: E 195 ASN cc_start: 0.8180 (t0) cc_final: 0.7672 (t0) REVERT: E 433 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.5487 (tmm160) REVERT: F 535 MET cc_start: 0.8679 (mmt) cc_final: 0.8372 (mmp) outliers start: 25 outliers final: 13 residues processed: 140 average time/residue: 0.1237 time to fit residues: 26.1309 Evaluate side-chains 125 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain F residue 603 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 122 optimal weight: 5.9990 chunk 77 optimal weight: 0.0040 chunk 102 optimal weight: 0.0770 chunk 47 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.078297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.065727 restraints weight = 59551.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067655 restraints weight = 33717.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068957 restraints weight = 22814.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.069844 restraints weight = 17221.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.070475 restraints weight = 14092.959| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15267 Z= 0.101 Angle : 0.573 11.312 20920 Z= 0.278 Chirality : 0.043 0.258 2585 Planarity : 0.003 0.028 2558 Dihedral : 5.250 76.257 3337 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.30 % Allowed : 8.57 % Favored : 90.12 % 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: 0.57 (0.21), residues: 1596 helix: 1.98 (0.29), residues: 363 sheet: 0.10 (0.26), residues: 391 loop : -0.13 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 192 TYR 0.012 0.001 TYR F 643 PHE 0.011 0.001 PHE C 53 TRP 0.031 0.002 TRP E 69 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00219 (15165) covalent geometry : angle 0.54689 (20649) SS BOND : bond 0.00198 ( 35) SS BOND : angle 0.79713 ( 70) hydrogen bonds : bond 0.03377 ( 442) hydrogen bonds : angle 4.77164 ( 1191) link_BETA1-4 : bond 0.00565 ( 13) link_BETA1-4 : angle 1.72785 ( 39) link_NAG-ASN : bond 0.00360 ( 54) link_NAG-ASN : angle 1.81122 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.8094 (mp0) cc_final: 0.7757 (mp0) REVERT: C 475 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.5369 (ppp) REVERT: C 478 ASN cc_start: 0.8094 (p0) cc_final: 0.7235 (p0) REVERT: C 479 TRP cc_start: 0.8241 (m-10) cc_final: 0.7186 (m-90) REVERT: D 584 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8238 (tm-30) REVERT: D 589 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8021 (t70) REVERT: D 650 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8630 (tt0) REVERT: A 84 ILE cc_start: 0.8182 (mt) cc_final: 0.7781 (mm) REVERT: B 530 MET cc_start: 0.6515 (mtm) cc_final: 0.5727 (ttm) REVERT: B 577 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8116 (tm-30) REVERT: B 581 LEU cc_start: 0.9145 (tp) cc_final: 0.8787 (tp) REVERT: B 584 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 626 MET cc_start: 0.6658 (ptp) cc_final: 0.6125 (mtm) REVERT: B 628 TRP cc_start: 0.8142 (m100) cc_final: 0.7383 (m100) REVERT: B 635 ILE cc_start: 0.8707 (pt) cc_final: 0.8282 (mm) REVERT: B 647 GLU cc_start: 0.8609 (pp20) cc_final: 0.8352 (pp20) REVERT: B 648 GLU cc_start: 0.8943 (tp30) cc_final: 0.8653 (tp30) REVERT: B 654 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8807 (tp30) REVERT: B 661 LEU cc_start: 0.6654 (tp) cc_final: 0.5981 (pp) REVERT: E 80 ASN cc_start: 0.8930 (t0) cc_final: 0.8116 (p0) REVERT: E 95 MET cc_start: 0.8684 (ptm) cc_final: 0.8143 (mtm) REVERT: E 195 ASN cc_start: 0.8173 (t0) cc_final: 0.7678 (t0) outliers start: 19 outliers final: 11 residues processed: 141 average time/residue: 0.1112 time to fit residues: 24.0253 Evaluate side-chains 126 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain F residue 522 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.077027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.064404 restraints weight = 59907.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066270 restraints weight = 34538.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067534 restraints weight = 23622.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068427 restraints weight = 17999.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068997 restraints weight = 14747.414| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15267 Z= 0.128 Angle : 0.586 12.029 20920 Z= 0.287 Chirality : 0.043 0.262 2585 Planarity : 0.003 0.029 2558 Dihedral : 5.011 61.087 3337 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.58 % Allowed : 9.12 % Favored : 89.30 % 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 (0.22), residues: 1596 helix: 2.00 (0.29), residues: 360 sheet: 0.11 (0.26), residues: 394 loop : -0.11 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 308 TYR 0.014 0.001 TYR E 39 PHE 0.025 0.001 PHE C 317 TRP 0.036 0.002 TRP E 69 HIS 0.003 0.001 HIS C 287 Details of bonding type rmsd covalent geometry : bond 0.00288 (15165) covalent geometry : angle 0.56000 (20649) SS BOND : bond 0.00315 ( 35) SS BOND : angle 0.91878 ( 70) hydrogen bonds : bond 0.03503 ( 442) hydrogen bonds : angle 4.76528 ( 1191) link_BETA1-4 : bond 0.00476 ( 13) link_BETA1-4 : angle 1.71418 ( 39) link_NAG-ASN : bond 0.00279 ( 54) link_NAG-ASN : angle 1.82306 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 475 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.5548 (ppp) REVERT: C 478 ASN cc_start: 0.8083 (p0) cc_final: 0.7213 (p0) REVERT: C 479 TRP cc_start: 0.8278 (m-10) cc_final: 0.7246 (m-90) REVERT: D 584 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8258 (tm-30) REVERT: D 589 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8055 (t70) REVERT: D 604 CYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7129 (p) REVERT: A 84 ILE cc_start: 0.8257 (mt) cc_final: 0.7843 (mm) REVERT: B 530 MET cc_start: 0.6625 (mtm) cc_final: 0.5517 (ttm) REVERT: B 577 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: B 581 LEU cc_start: 0.9140 (tp) cc_final: 0.8866 (tp) REVERT: B 625 ASN cc_start: 0.6905 (p0) cc_final: 0.6573 (p0) REVERT: B 626 MET cc_start: 0.6826 (ptp) cc_final: 0.6510 (mpp) REVERT: B 628 TRP cc_start: 0.8302 (m100) cc_final: 0.7474 (m100) REVERT: B 647 GLU cc_start: 0.8667 (pp20) cc_final: 0.8415 (pp20) REVERT: B 648 GLU cc_start: 0.8984 (tp30) cc_final: 0.8657 (tp30) REVERT: B 654 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8837 (mm-30) REVERT: E 80 ASN cc_start: 0.8966 (t0) cc_final: 0.8152 (p0) REVERT: E 95 MET cc_start: 0.8692 (ptm) cc_final: 0.8211 (mtm) REVERT: E 195 ASN cc_start: 0.8192 (t0) cc_final: 0.7714 (t0) outliers start: 23 outliers final: 14 residues processed: 126 average time/residue: 0.1145 time to fit residues: 22.3437 Evaluate side-chains 125 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain F residue 603 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 60 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.0000 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.075369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.062682 restraints weight = 60195.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.064549 restraints weight = 34107.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.065835 restraints weight = 23119.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.066742 restraints weight = 17558.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.067332 restraints weight = 14301.640| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15267 Z= 0.158 Angle : 0.605 11.349 20920 Z= 0.296 Chirality : 0.044 0.265 2585 Planarity : 0.003 0.030 2558 Dihedral : 4.938 50.873 3337 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.58 % Allowed : 9.26 % Favored : 89.16 % 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: 0.50 (0.22), residues: 1596 helix: 1.89 (0.29), residues: 363 sheet: 0.08 (0.27), residues: 389 loop : -0.17 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 480 TYR 0.014 0.002 TYR B 638 PHE 0.012 0.001 PHE C 317 TRP 0.027 0.002 TRP C 428 HIS 0.004 0.001 HIS C 287 Details of bonding type rmsd covalent geometry : bond 0.00359 (15165) covalent geometry : angle 0.57723 (20649) SS BOND : bond 0.00323 ( 35) SS BOND : angle 0.95876 ( 70) hydrogen bonds : bond 0.03582 ( 442) hydrogen bonds : angle 4.83127 ( 1191) link_BETA1-4 : bond 0.00467 ( 13) link_BETA1-4 : angle 1.69878 ( 39) link_NAG-ASN : bond 0.00276 ( 54) link_NAG-ASN : angle 1.93643 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 478 ASN cc_start: 0.8164 (p0) cc_final: 0.7930 (p0) REVERT: D 584 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8253 (tm-30) REVERT: D 589 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8124 (t70) REVERT: A 84 ILE cc_start: 0.8336 (mt) cc_final: 0.7948 (mm) REVERT: A 104 MET cc_start: 0.8971 (tmm) cc_final: 0.8698 (tmm) REVERT: B 577 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8168 (tm-30) REVERT: B 581 LEU cc_start: 0.9166 (tp) cc_final: 0.8787 (tp) REVERT: B 625 ASN cc_start: 0.6923 (p0) cc_final: 0.6610 (p0) REVERT: B 626 MET cc_start: 0.6908 (ptp) cc_final: 0.6541 (mpp) REVERT: B 628 TRP cc_start: 0.8353 (m100) cc_final: 0.7695 (m100) REVERT: B 647 GLU cc_start: 0.8637 (pp20) cc_final: 0.8392 (pp20) REVERT: B 648 GLU cc_start: 0.8966 (tp30) cc_final: 0.8635 (tp30) REVERT: E 80 ASN cc_start: 0.8896 (t0) cc_final: 0.8107 (p0) REVERT: E 95 MET cc_start: 0.8734 (ptm) cc_final: 0.8364 (mtm) REVERT: E 195 ASN cc_start: 0.8173 (t0) cc_final: 0.7702 (t0) outliers start: 23 outliers final: 16 residues processed: 125 average time/residue: 0.1190 time to fit residues: 22.9477 Evaluate side-chains 121 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 426 ASN Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain F residue 603 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 123 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.076030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.063281 restraints weight = 60405.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065201 restraints weight = 33970.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.066515 restraints weight = 22959.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.067381 restraints weight = 17311.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068048 restraints weight = 14206.240| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15267 Z= 0.110 Angle : 0.571 8.952 20920 Z= 0.283 Chirality : 0.043 0.256 2585 Planarity : 0.003 0.030 2558 Dihedral : 4.501 38.795 3337 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.23 % Allowed : 10.01 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.54 (0.22), residues: 1596 helix: 2.02 (0.29), residues: 367 sheet: 0.17 (0.27), residues: 387 loop : -0.24 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 308 TYR 0.020 0.001 TYR A 39 PHE 0.059 0.001 PHE C 317 TRP 0.018 0.002 TRP L 36 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00250 (15165) covalent geometry : angle 0.54543 (20649) SS BOND : bond 0.00336 ( 35) SS BOND : angle 0.80814 ( 70) hydrogen bonds : bond 0.03344 ( 442) hydrogen bonds : angle 4.67529 ( 1191) link_BETA1-4 : bond 0.00488 ( 13) link_BETA1-4 : angle 1.57040 ( 39) link_NAG-ASN : bond 0.00295 ( 54) link_NAG-ASN : angle 1.81863 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 208 VAL cc_start: 0.9315 (OUTLIER) cc_final: 0.8983 (m) REVERT: C 478 ASN cc_start: 0.8121 (p0) cc_final: 0.7898 (p0) REVERT: D 574 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8725 (mtmt) REVERT: D 584 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8239 (tm-30) REVERT: D 589 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8169 (t70) REVERT: A 84 ILE cc_start: 0.8313 (mt) cc_final: 0.7944 (mm) REVERT: A 104 MET cc_start: 0.8972 (tmm) cc_final: 0.8614 (tmm) REVERT: B 530 MET cc_start: 0.6692 (mtm) cc_final: 0.5620 (mtt) REVERT: B 577 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: B 581 LEU cc_start: 0.9159 (tp) cc_final: 0.8855 (tp) REVERT: B 590 GLN cc_start: 0.9234 (tp40) cc_final: 0.8994 (mm-40) REVERT: B 625 ASN cc_start: 0.7058 (p0) cc_final: 0.6704 (p0) REVERT: B 626 MET cc_start: 0.6830 (ptp) cc_final: 0.6545 (mpp) REVERT: B 628 TRP cc_start: 0.8256 (m100) cc_final: 0.7716 (m100) REVERT: B 642 ILE cc_start: 0.9204 (mt) cc_final: 0.8528 (tt) REVERT: B 647 GLU cc_start: 0.8590 (pp20) cc_final: 0.8324 (pp20) REVERT: B 648 GLU cc_start: 0.8949 (tp30) cc_final: 0.8622 (tp30) REVERT: E 80 ASN cc_start: 0.8893 (t0) cc_final: 0.8234 (p0) REVERT: E 95 MET cc_start: 0.8657 (ptm) cc_final: 0.8452 (mtm) REVERT: E 195 ASN cc_start: 0.8144 (t0) cc_final: 0.7681 (t0) outliers start: 18 outliers final: 14 residues processed: 122 average time/residue: 0.1163 time to fit residues: 21.9431 Evaluate side-chains 124 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain F residue 603 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.075455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.062683 restraints weight = 60546.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.064564 restraints weight = 34266.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065860 restraints weight = 23266.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066720 restraints weight = 17651.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.067380 restraints weight = 14495.319| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15267 Z= 0.127 Angle : 0.574 8.609 20920 Z= 0.283 Chirality : 0.043 0.260 2585 Planarity : 0.003 0.030 2558 Dihedral : 4.475 39.106 3337 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.30 % Allowed : 10.29 % Favored : 88.41 % 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: 0.50 (0.22), residues: 1596 helix: 1.98 (0.29), residues: 363 sheet: -0.00 (0.26), residues: 410 loop : -0.16 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 308 TYR 0.021 0.001 TYR B 638 PHE 0.023 0.001 PHE C 317 TRP 0.029 0.002 TRP C 428 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00288 (15165) covalent geometry : angle 0.54831 (20649) SS BOND : bond 0.00265 ( 35) SS BOND : angle 0.87314 ( 70) hydrogen bonds : bond 0.03357 ( 442) hydrogen bonds : angle 4.70220 ( 1191) link_BETA1-4 : bond 0.00376 ( 13) link_BETA1-4 : angle 1.61225 ( 39) link_NAG-ASN : bond 0.00273 ( 54) link_NAG-ASN : angle 1.79683 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 208 VAL cc_start: 0.9312 (OUTLIER) cc_final: 0.8981 (m) REVERT: C 478 ASN cc_start: 0.8119 (p0) cc_final: 0.7899 (p0) REVERT: D 584 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8235 (tm-30) REVERT: D 589 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8215 (t70) REVERT: A 84 ILE cc_start: 0.8295 (mt) cc_final: 0.7940 (mm) REVERT: A 104 MET cc_start: 0.8991 (tmm) cc_final: 0.8704 (tmm) REVERT: B 530 MET cc_start: 0.6750 (mtm) cc_final: 0.5320 (ttm) REVERT: B 577 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: B 581 LEU cc_start: 0.9113 (tp) cc_final: 0.8766 (tp) REVERT: B 590 GLN cc_start: 0.9249 (tp40) cc_final: 0.9005 (mm-40) REVERT: B 625 ASN cc_start: 0.7108 (p0) cc_final: 0.6842 (p0) REVERT: B 626 MET cc_start: 0.6886 (ptp) cc_final: 0.6579 (mpp) REVERT: B 628 TRP cc_start: 0.8278 (m100) cc_final: 0.7714 (m100) REVERT: B 647 GLU cc_start: 0.8611 (pp20) cc_final: 0.8308 (pp20) REVERT: B 654 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8537 (tp30) REVERT: E 80 ASN cc_start: 0.8842 (t0) cc_final: 0.8221 (p0) REVERT: E 95 MET cc_start: 0.8687 (ptm) cc_final: 0.8456 (mtm) REVERT: E 195 ASN cc_start: 0.8101 (t0) cc_final: 0.7654 (t0) REVERT: F 542 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8397 (ttp80) outliers start: 19 outliers final: 14 residues processed: 119 average time/residue: 0.1245 time to fit residues: 22.5249 Evaluate side-chains 122 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain F residue 603 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 50 optimal weight: 0.6980 chunk 109 optimal weight: 0.0470 chunk 76 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 0.0670 chunk 95 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.076151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.063413 restraints weight = 60520.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.065330 restraints weight = 34066.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066637 restraints weight = 23033.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067541 restraints weight = 17413.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068199 restraints weight = 14199.079| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15267 Z= 0.101 Angle : 0.570 9.165 20920 Z= 0.282 Chirality : 0.043 0.252 2585 Planarity : 0.003 0.029 2558 Dihedral : 4.375 38.403 3337 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.30 % Allowed : 10.22 % Favored : 88.48 % 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: 0.55 (0.22), residues: 1596 helix: 2.10 (0.29), residues: 363 sheet: 0.08 (0.26), residues: 418 loop : -0.21 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 579 TYR 0.017 0.001 TYR B 638 PHE 0.024 0.001 PHE C 317 TRP 0.029 0.001 TRP C 428 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00226 (15165) covalent geometry : angle 0.54698 (20649) SS BOND : bond 0.00240 ( 35) SS BOND : angle 0.82956 ( 70) hydrogen bonds : bond 0.03295 ( 442) hydrogen bonds : angle 4.66656 ( 1191) link_BETA1-4 : bond 0.00481 ( 13) link_BETA1-4 : angle 1.53637 ( 39) link_NAG-ASN : bond 0.00300 ( 54) link_NAG-ASN : angle 1.73176 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 154 MET cc_start: 0.8733 (mmm) cc_final: 0.8193 (ttm) REVERT: C 208 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.8974 (m) REVERT: C 427 MET cc_start: 0.8017 (ttm) cc_final: 0.7732 (ttt) REVERT: C 478 ASN cc_start: 0.8075 (p0) cc_final: 0.7871 (p0) REVERT: D 574 LYS cc_start: 0.9224 (mmmt) cc_final: 0.8734 (mtmt) REVERT: D 584 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8203 (tm-30) REVERT: D 589 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8114 (t70) REVERT: A 84 ILE cc_start: 0.8278 (mt) cc_final: 0.7948 (mm) REVERT: A 104 MET cc_start: 0.8969 (tmm) cc_final: 0.8648 (tmm) REVERT: B 530 MET cc_start: 0.6830 (mtm) cc_final: 0.5523 (ttm) REVERT: B 535 MET cc_start: 0.7306 (tpt) cc_final: 0.6991 (tmm) REVERT: B 577 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: B 581 LEU cc_start: 0.9126 (tp) cc_final: 0.8854 (tp) REVERT: B 590 GLN cc_start: 0.9244 (tp40) cc_final: 0.9040 (mm-40) REVERT: B 625 ASN cc_start: 0.7192 (p0) cc_final: 0.6936 (p0) REVERT: B 626 MET cc_start: 0.6973 (ptp) cc_final: 0.6736 (mpp) REVERT: B 628 TRP cc_start: 0.8249 (m100) cc_final: 0.7690 (m100) REVERT: B 633 LYS cc_start: 0.8912 (mmtm) cc_final: 0.8512 (mmtm) REVERT: B 647 GLU cc_start: 0.8602 (pp20) cc_final: 0.8284 (pp20) REVERT: B 654 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8247 (tp30) REVERT: E 80 ASN cc_start: 0.8838 (t0) cc_final: 0.8226 (p0) REVERT: E 95 MET cc_start: 0.8629 (ptm) cc_final: 0.8382 (mtm) REVERT: E 195 ASN cc_start: 0.8064 (t0) cc_final: 0.7648 (t0) REVERT: E 246 GLN cc_start: 0.7573 (tp40) cc_final: 0.7306 (tp-100) REVERT: E 435 MET cc_start: 0.8404 (mtp) cc_final: 0.8147 (mtt) REVERT: F 542 ARG cc_start: 0.8616 (ttp80) cc_final: 0.8388 (ttp80) outliers start: 19 outliers final: 14 residues processed: 121 average time/residue: 0.1257 time to fit residues: 23.1216 Evaluate side-chains 124 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain F residue 603 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 96 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.074741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.062119 restraints weight = 60606.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063894 restraints weight = 35540.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065108 restraints weight = 24696.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.065974 restraints weight = 19079.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066501 restraints weight = 15712.238| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15267 Z= 0.148 Angle : 0.596 10.321 20920 Z= 0.293 Chirality : 0.043 0.260 2585 Planarity : 0.003 0.030 2558 Dihedral : 4.487 39.573 3337 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.30 % Allowed : 10.22 % Favored : 88.48 % 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: 0.50 (0.22), residues: 1596 helix: 2.06 (0.29), residues: 363 sheet: 0.02 (0.26), residues: 418 loop : -0.23 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 579 TYR 0.017 0.002 TYR B 638 PHE 0.022 0.002 PHE C 317 TRP 0.023 0.002 TRP D 623 HIS 0.004 0.001 HIS C 287 Details of bonding type rmsd covalent geometry : bond 0.00335 (15165) covalent geometry : angle 0.57172 (20649) SS BOND : bond 0.00285 ( 35) SS BOND : angle 0.87896 ( 70) hydrogen bonds : bond 0.03507 ( 442) hydrogen bonds : angle 4.70413 ( 1191) link_BETA1-4 : bond 0.00437 ( 13) link_BETA1-4 : angle 1.60944 ( 39) link_NAG-ASN : bond 0.00269 ( 54) link_NAG-ASN : angle 1.79025 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2168.98 seconds wall clock time: 38 minutes 34.75 seconds (2314.75 seconds total)