Starting phenix.real_space_refine on Thu Sep 18 08:01:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nhi_49412/09_2025/9nhi_49412.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nhi_49412/09_2025/9nhi_49412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nhi_49412/09_2025/9nhi_49412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nhi_49412/09_2025/9nhi_49412.map" model { file = "/net/cci-nas-00/data/ceres_data/9nhi_49412/09_2025/9nhi_49412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nhi_49412/09_2025/9nhi_49412.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 9383 2.51 5 N 2519 2.21 5 O 3020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15028 Number of models: 1 Model: "" Number of chains: 26 Chain: "H" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 615 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'TRANS': 118} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'UNK:plan-1': 115} Unresolved non-hydrogen planarities: 115 Chain: "L" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 502 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'TRANS': 96} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'UNK:plan-1': 93} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3457 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "B" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 945 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3120 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 21, 'TRANS': 371} Chain breaks: 6 Chain: "E" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 955 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "D" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3450 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 955 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "G" 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: "I" 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: "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: 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: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" 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: "O" 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: "P" 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: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" 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: "S" 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: "T" 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: "U" 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 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: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" 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: "D" 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 Time building chain proxies: 3.89, per 1000 atoms: 0.26 Number of scatterers: 15028 At special positions: 0 Unit cell: (130.625, 120.175, 146.3, 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 106 16.00 O 3020 8.00 N 2519 7.00 C 9383 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 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 20 " - pdb=" SG CYS L 85 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS F 664 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 664 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 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=2.04 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 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 664 " - pdb=" SG CYS D 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " 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 ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA Q 3 " - " MAN Q 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 301 " " NAG A 603 " - " ASN A 295 " " NAG A 604 " - " ASN A 160 " " NAG A 605 " - " ASN A 130 " " NAG A 606 " - " ASN A 197 " " NAG A 607 " - " ASN A 230 " " NAG A 608 " - " ASN A 289 " " NAG A 609 " - " ASN A 339 " " NAG A 610 " - " ASN A 386 " " NAG A 611 " - " ASN A 392 " " NAG A 612 " - " ASN A 398 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 616 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 241 " " NAG C 602 " - " ASN C 130 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 160 " " NAG C 605 " - " ASN C 386 " " NAG C 606 " - " ASN C 197 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 339 " " NAG C 609 " - " ASN C 88 " " NAG C 610 " - " ASN C 230 " " NAG C 611 " - " ASN C 234 " " NAG D 601 " - " ASN D 197 " " NAG D 602 " - " ASN D 160 " " NAG D 603 " - " ASN D 230 " " NAG D 604 " - " ASN D 234 " " NAG D 605 " - " ASN D 276 " " NAG D 606 " - " ASN D 289 " " NAG D 607 " - " ASN D 448 " " NAG D 608 " - " ASN D 295 " " NAG D 609 " - " ASN D 413 " " NAG D 610 " - " ASN D 332 " " NAG D 611 " - " ASN D 301 " " NAG D 612 " - " ASN D 386 " " NAG D 613 " - " ASN D 392 " " NAG D 614 " - " ASN D 398 " " NAG D 615 " - " ASN D 130 " " NAG E 701 " - " ASN E 656 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 332 " " NAG J 1 " - " ASN A 413 " " NAG K 1 " - " ASN A 448 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN C 448 " " NAG O 1 " - " ASN C 295 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN C 262 " " NAG R 1 " - " ASN C 413 " " NAG S 1 " - " ASN D 241 " " NAG T 1 " - " ASN D 156 " " NAG U 1 " - " ASN D 262 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 527.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3486 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 25 sheets defined 26.9% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'H' and resid 27 through 31 removed outlier: 3.690A pdb=" N UNK H 31 " --> pdb=" O UNK H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 Processing helix chain 'H' and resid 70 through 74 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'L' and resid 64 through 68 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.953A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.148A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.330A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 4.149A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.802A pdb=" N LYS B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 659 Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.861A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.951A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 533 removed outlier: 3.575A pdb=" N ALA E 533 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 541 Processing helix chain 'E' and resid 572 through 596 Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 660 Processing helix chain 'E' and resid 661 through 664 Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 98 through 116 removed outlier: 3.842A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 476 through 481 removed outlier: 3.878A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.396A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.583A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 659 removed outlier: 3.744A pdb=" N GLU F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 16 through 21 removed outlier: 4.480A pdb=" N UNK H 16 " --> pdb=" O UNK H 82 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N UNK H 82 " --> pdb=" O UNK H 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 54 through 58 removed outlier: 3.695A pdb=" N UNK H 54 " --> pdb=" O UNK H 51 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N UNK H 56 " --> pdb=" O UNK H 49 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N UNK H 49 " --> pdb=" O UNK H 56 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N UNK H 58 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N UNK H 47 " --> pdb=" O UNK H 58 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N UNK H 46 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N UNK H 37 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N UNK H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP H 35 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N UNK H 50 " --> pdb=" O UNK H 33 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N UNK H 33 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS H 93 " --> pdb=" O UNK H 114 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N UNK H 114 " --> pdb=" O CYS H 93 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N UNK H 95 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TRP H 112 " --> pdb=" O UNK H 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 41 through 46 removed outlier: 6.530A pdb=" N TRP L 32 " --> pdb=" O UNK L 44 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N UNK L 46 " --> pdb=" O UNK L 30 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N UNK L 30 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N UNK L 93 " --> pdb=" O UNK L 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.925A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.487A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.105A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA8, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA9, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AB2, 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: 6.738A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A 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 465 through 470 Processing sheet with id=AB3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.177A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.513A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 removed outlier: 4.526A pdb=" N SER C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 200 through 202 Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 283 through 285 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 283 through 285 current: chain 'C' and resid 315 through 323A WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 removed outlier: 4.000A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.037A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.599A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.956A pdb=" N VAL D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR D 435 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 259 through 261 current: chain 'D' and resid 284 through 308 removed outlier: 6.629A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 316 through 323A current: chain 'D' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 381 through 385 current: chain 'D' and resid 465 through 470 451 hydrogen bonds defined for protein. 1239 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: 2.54 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4730 1.35 - 1.47: 3838 1.47 - 1.60: 6587 1.60 - 1.73: 0 1.73 - 1.85: 139 Bond restraints: 15294 Sorted by residual: bond pdb=" CG1 ILE A 424 " pdb=" CD1 ILE A 424 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.90e+00 bond pdb=" C CYS A 205 " pdb=" N PRO A 206 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.08e+00 bond pdb=" C UNK H 52 " pdb=" N UNK H 53 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.40e-02 5.10e+03 3.01e+00 bond pdb=" CB CYS D 205 " pdb=" SG CYS D 205 " ideal model delta sigma weight residual 1.808 1.854 -0.046 3.30e-02 9.18e+02 1.92e+00 bond pdb=" CB ILE A 184 " pdb=" CG2 ILE A 184 " ideal model delta sigma weight residual 1.521 1.566 -0.045 3.30e-02 9.18e+02 1.86e+00 ... (remaining 15289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 19340 1.77 - 3.54: 1284 3.54 - 5.31: 150 5.31 - 7.08: 27 7.08 - 8.85: 3 Bond angle restraints: 20804 Sorted by residual: angle pdb=" N GLU A 482 " pdb=" CA GLU A 482 " pdb=" C GLU A 482 " ideal model delta sigma weight residual 109.69 100.91 8.78 1.44e+00 4.82e-01 3.72e+01 angle pdb=" N LEU D 390 " pdb=" CA LEU D 390 " pdb=" C LEU D 390 " ideal model delta sigma weight residual 110.42 101.57 8.85 1.55e+00 4.16e-01 3.26e+01 angle pdb=" N GLU C 293 " pdb=" CA GLU C 293 " pdb=" C GLU C 293 " ideal model delta sigma weight residual 109.96 103.58 6.38 1.50e+00 4.44e-01 1.81e+01 angle pdb=" N CYS C 196 " pdb=" CA CYS C 196 " pdb=" C CYS C 196 " ideal model delta sigma weight residual 111.11 115.47 -4.36 1.20e+00 6.94e-01 1.32e+01 angle pdb=" N TRP F 596 " pdb=" CA TRP F 596 " pdb=" C TRP F 596 " ideal model delta sigma weight residual 110.55 105.68 4.87 1.35e+00 5.49e-01 1.30e+01 ... (remaining 20799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.67: 9934 24.67 - 49.34: 176 49.34 - 74.02: 44 74.02 - 98.69: 23 98.69 - 123.36: 11 Dihedral angle restraints: 10188 sinusoidal: 4836 harmonic: 5352 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 145.42 -52.42 1 1.00e+01 1.00e-02 3.74e+01 dihedral pdb=" CB CYS B 664 " pdb=" SG CYS B 664 " pdb=" SG CYS C 501 " pdb=" CB CYS C 501 " ideal model delta sinusoidal sigma weight residual -86.00 -130.53 44.53 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -123.83 37.83 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 10185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2320 0.097 - 0.194: 278 0.194 - 0.290: 11 0.290 - 0.387: 1 0.387 - 0.484: 2 Chirality restraints: 2612 Sorted by residual: chirality pdb=" C1 NAG C 608 " pdb=" ND2 ASN C 339 " pdb=" C2 NAG C 608 " pdb=" O5 NAG C 608 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" C1 NAG D 606 " pdb=" ND2 ASN D 289 " pdb=" C2 NAG D 606 " pdb=" O5 NAG D 606 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" C1 NAG A 608 " pdb=" ND2 ASN A 289 " pdb=" C2 NAG A 608 " pdb=" O5 NAG A 608 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 2609 not shown) Planarity restraints: 2617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 538 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C THR F 538 " 0.063 2.00e-02 2.50e+03 pdb=" O THR F 538 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL F 539 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 640 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C ASN B 640 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN B 640 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU B 641 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 639 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C THR B 639 " -0.060 2.00e-02 2.50e+03 pdb=" O THR B 639 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN B 640 " 0.020 2.00e-02 2.50e+03 ... (remaining 2614 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2785 2.78 - 3.31: 13448 3.31 - 3.84: 24458 3.84 - 4.37: 28626 4.37 - 4.90: 48995 Nonbonded interactions: 118312 Sorted by model distance: nonbonded pdb=" NZ LYS C 282 " pdb=" OD2 ASP C 477 " model vdw 2.249 3.120 nonbonded pdb=" OD1 ASP C 113 " pdb=" NZ LYS C 432 " model vdw 2.252 3.120 nonbonded pdb=" NH1 ARG C 503 " pdb=" OE1 GLN E 650 " model vdw 2.258 3.120 nonbonded pdb=" OE2 GLU A 370 " pdb=" NZ LYS A 421 " model vdw 2.287 3.120 nonbonded pdb=" O LEU F 661 " pdb=" OG1 THR F 662 " model vdw 2.340 3.040 ... (remaining 118307 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 33 through 275 or resid 281 through 353 or resid 369 throu \ gh 396 or resid 413 through 455 or resid 475 through 504 or resid 602 through 61 \ 2)) selection = chain 'C' selection = (chain 'D' and (resid 33 through 275 or resid 281 through 353 or resid 369 throu \ gh 396 or resid 413 through 455 or resid 475 through 504 or resid 603 through 61 \ 3)) } ncs_group { reference = (chain 'B' and (resid 521 through 546 or resid 572 through 664)) selection = (chain 'E' and (resid 521 through 546 or resid 572 through 664)) selection = (chain 'F' and (resid 521 through 546 or resid 572 through 664)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'M' selection = chain 'Q' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.810 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.005 0.077 15404 Z= 0.221 Angle : 0.993 10.861 21099 Z= 0.539 Chirality : 0.061 0.484 2612 Planarity : 0.005 0.052 2562 Dihedral : 11.530 123.361 6597 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.59 (0.19), residues: 1586 helix: 0.45 (0.24), residues: 361 sheet: 0.80 (0.23), residues: 432 loop : 0.27 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 192 TYR 0.017 0.002 TYR E 643 PHE 0.023 0.003 PHE A 383 TRP 0.031 0.004 TRP D 479 HIS 0.006 0.002 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00502 (15294) covalent geometry : angle 0.96466 (20804) SS BOND : bond 0.00447 ( 35) SS BOND : angle 2.23638 ( 70) hydrogen bonds : bond 0.12626 ( 451) hydrogen bonds : angle 6.72515 ( 1239) link_ALPHA1-3 : bond 0.00377 ( 2) link_ALPHA1-3 : angle 1.87541 ( 6) link_ALPHA1-6 : bond 0.00694 ( 2) link_ALPHA1-6 : angle 1.31700 ( 6) link_BETA1-4 : bond 0.00828 ( 16) link_BETA1-4 : angle 2.31752 ( 48) link_NAG-ASN : bond 0.00471 ( 55) link_NAG-ASN : angle 2.18719 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6887 (mp0) REVERT: A 279 ASP cc_start: 0.8709 (t0) cc_final: 0.8453 (t0) REVERT: A 363 GLN cc_start: 0.8313 (pm20) cc_final: 0.7904 (tp-100) REVERT: B 585 HIS cc_start: 0.8627 (m170) cc_final: 0.8414 (m170) REVERT: B 655 LYS cc_start: 0.7518 (mttt) cc_final: 0.7155 (pttm) REVERT: C 46 LYS cc_start: 0.8953 (pttt) cc_final: 0.8699 (ptpt) REVERT: C 78 ASP cc_start: 0.7364 (t0) cc_final: 0.7062 (t0) REVERT: C 227 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8561 (tttm) REVERT: E 629 MET cc_start: 0.9220 (mmm) cc_final: 0.8920 (mmm) REVERT: E 640 ASN cc_start: 0.8262 (m-40) cc_final: 0.7982 (m-40) REVERT: E 647 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8535 (mt-10) REVERT: D 207 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7560 (tptt) REVERT: D 432 LYS cc_start: 0.8378 (mtpt) cc_final: 0.7918 (tmtt) REVERT: F 632 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7710 (mm-30) REVERT: F 655 LYS cc_start: 0.6865 (mttt) cc_final: 0.6572 (pttm) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1486 time to fit residues: 71.9443 Evaluate side-chains 179 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 644 ASN C 92 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 GLN D 170 GLN F 575 GLN F 585 HIS F 644 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.130135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.100829 restraints weight = 23934.871| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.43 r_work: 0.3190 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15404 Z= 0.168 Angle : 0.621 14.371 21099 Z= 0.309 Chirality : 0.045 0.277 2612 Planarity : 0.003 0.036 2562 Dihedral : 8.615 102.566 3490 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.50 % Allowed : 5.81 % Favored : 92.69 % 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: 0.86 (0.21), residues: 1586 helix: 1.56 (0.27), residues: 365 sheet: 0.62 (0.24), residues: 437 loop : 0.17 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 503 TYR 0.016 0.001 TYR C 217 PHE 0.019 0.002 PHE C 353 TRP 0.021 0.002 TRP C 479 HIS 0.006 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00393 (15294) covalent geometry : angle 0.58971 (20804) SS BOND : bond 0.00308 ( 35) SS BOND : angle 1.21730 ( 70) hydrogen bonds : bond 0.04444 ( 451) hydrogen bonds : angle 5.20842 ( 1239) link_ALPHA1-3 : bond 0.00650 ( 2) link_ALPHA1-3 : angle 2.29232 ( 6) link_ALPHA1-6 : bond 0.00442 ( 2) link_ALPHA1-6 : angle 1.68660 ( 6) link_BETA1-4 : bond 0.00557 ( 16) link_BETA1-4 : angle 1.81493 ( 48) link_NAG-ASN : bond 0.00327 ( 55) link_NAG-ASN : angle 1.89770 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 363 GLN cc_start: 0.8524 (pm20) cc_final: 0.8020 (tp-100) REVERT: A 462 ASN cc_start: 0.7928 (m-40) cc_final: 0.7723 (p0) REVERT: A 479 TRP cc_start: 0.8146 (m-10) cc_final: 0.7888 (m-10) REVERT: B 592 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8732 (mp) REVERT: B 634 GLU cc_start: 0.8237 (tt0) cc_final: 0.7948 (tt0) REVERT: B 655 LYS cc_start: 0.7691 (mttt) cc_final: 0.7376 (pttm) REVERT: C 46 LYS cc_start: 0.8962 (pttt) cc_final: 0.8720 (ptpt) REVERT: C 82 GLN cc_start: 0.8157 (pm20) cc_final: 0.7905 (pp30) REVERT: C 227 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8496 (tttt) REVERT: E 577 GLN cc_start: 0.8444 (tt0) cc_final: 0.8225 (tt0) REVERT: E 647 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8577 (mt-10) REVERT: D 83 GLU cc_start: 0.8087 (tt0) cc_final: 0.7841 (tt0) REVERT: D 207 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7779 (tptt) REVERT: F 543 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7565 (tm-30) REVERT: F 575 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7023 (tp40) REVERT: F 655 LYS cc_start: 0.6635 (mttt) cc_final: 0.6353 (tmmt) REVERT: F 659 GLU cc_start: 0.6494 (pt0) cc_final: 0.6287 (pt0) outliers start: 22 outliers final: 15 residues processed: 222 average time/residue: 0.1293 time to fit residues: 42.3149 Evaluate side-chains 180 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 52 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 0.0000 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 0.0770 chunk 22 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.6344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN F 644 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100175 restraints weight = 24050.640| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.46 r_work: 0.3188 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15404 Z= 0.129 Angle : 0.546 11.764 21099 Z= 0.270 Chirality : 0.044 0.325 2612 Planarity : 0.003 0.034 2562 Dihedral : 7.602 99.886 3490 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.71 % Allowed : 7.04 % Favored : 91.25 % 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: 0.79 (0.21), residues: 1586 helix: 1.83 (0.27), residues: 364 sheet: 0.58 (0.24), residues: 430 loop : -0.05 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.011 0.001 TYR E 638 PHE 0.014 0.002 PHE A 53 TRP 0.020 0.001 TRP A 479 HIS 0.006 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00297 (15294) covalent geometry : angle 0.51791 (20804) SS BOND : bond 0.00344 ( 35) SS BOND : angle 1.10084 ( 70) hydrogen bonds : bond 0.03818 ( 451) hydrogen bonds : angle 4.72216 ( 1239) link_ALPHA1-3 : bond 0.01003 ( 2) link_ALPHA1-3 : angle 1.77349 ( 6) link_ALPHA1-6 : bond 0.00804 ( 2) link_ALPHA1-6 : angle 1.67483 ( 6) link_BETA1-4 : bond 0.00540 ( 16) link_BETA1-4 : angle 1.65325 ( 48) link_NAG-ASN : bond 0.00292 ( 55) link_NAG-ASN : angle 1.68285 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 363 GLN cc_start: 0.8560 (pm20) cc_final: 0.8164 (tp40) REVERT: A 479 TRP cc_start: 0.8008 (m-10) cc_final: 0.7657 (m-10) REVERT: B 592 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8779 (mp) REVERT: B 634 GLU cc_start: 0.8228 (tt0) cc_final: 0.7984 (tt0) REVERT: B 655 LYS cc_start: 0.7739 (mttt) cc_final: 0.7532 (pttm) REVERT: C 78 ASP cc_start: 0.7564 (t0) cc_final: 0.7362 (t0) REVERT: C 100 MET cc_start: 0.9342 (mtp) cc_final: 0.9086 (mtp) REVERT: C 227 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8494 (tttm) REVERT: E 629 MET cc_start: 0.9240 (mmm) cc_final: 0.8748 (mmm) REVERT: D 95 MET cc_start: 0.8943 (ptm) cc_final: 0.8712 (ptm) REVERT: D 207 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7824 (tptt) REVERT: F 543 GLN cc_start: 0.8433 (mm-40) cc_final: 0.7696 (tm-30) REVERT: F 575 GLN cc_start: 0.7577 (mm-40) cc_final: 0.6977 (tp40) outliers start: 25 outliers final: 19 residues processed: 199 average time/residue: 0.1328 time to fit residues: 38.0207 Evaluate side-chains 180 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 85 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 107 optimal weight: 0.0030 chunk 75 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 40 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 591 GLN F 644 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100412 restraints weight = 24098.528| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.46 r_work: 0.3186 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15404 Z= 0.113 Angle : 0.525 10.891 21099 Z= 0.258 Chirality : 0.044 0.297 2612 Planarity : 0.003 0.034 2562 Dihedral : 7.044 98.692 3490 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.98 % Allowed : 7.93 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.21), residues: 1586 helix: 1.94 (0.28), residues: 365 sheet: 0.62 (0.24), residues: 428 loop : -0.16 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 542 TYR 0.011 0.001 TYR E 638 PHE 0.014 0.001 PHE A 53 TRP 0.014 0.001 TRP D 479 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00258 (15294) covalent geometry : angle 0.49640 (20804) SS BOND : bond 0.00366 ( 35) SS BOND : angle 1.02961 ( 70) hydrogen bonds : bond 0.03544 ( 451) hydrogen bonds : angle 4.50154 ( 1239) link_ALPHA1-3 : bond 0.01098 ( 2) link_ALPHA1-3 : angle 1.99746 ( 6) link_ALPHA1-6 : bond 0.00926 ( 2) link_ALPHA1-6 : angle 1.79469 ( 6) link_BETA1-4 : bond 0.00507 ( 16) link_BETA1-4 : angle 1.56120 ( 48) link_NAG-ASN : bond 0.00285 ( 55) link_NAG-ASN : angle 1.64186 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 244 THR cc_start: 0.8492 (m) cc_final: 0.8279 (m) REVERT: A 363 GLN cc_start: 0.8505 (pm20) cc_final: 0.8062 (tp40) REVERT: A 479 TRP cc_start: 0.8008 (m-10) cc_final: 0.7583 (m-10) REVERT: B 634 GLU cc_start: 0.8256 (tt0) cc_final: 0.8010 (tt0) REVERT: B 655 LYS cc_start: 0.7704 (mttt) cc_final: 0.7498 (pttm) REVERT: C 82 GLN cc_start: 0.7923 (pm20) cc_final: 0.7625 (pp30) REVERT: C 100 MET cc_start: 0.9337 (mtp) cc_final: 0.9041 (mtp) REVERT: C 227 LYS cc_start: 0.8635 (ttpt) cc_final: 0.8356 (tttm) REVERT: D 83 GLU cc_start: 0.8101 (tt0) cc_final: 0.7884 (tt0) REVERT: D 95 MET cc_start: 0.8991 (ptm) cc_final: 0.8763 (ptm) REVERT: D 207 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7840 (tptt) REVERT: F 543 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7597 (tm-30) REVERT: F 575 GLN cc_start: 0.7574 (mm-40) cc_final: 0.6938 (tp40) outliers start: 29 outliers final: 20 residues processed: 191 average time/residue: 0.1296 time to fit residues: 36.6125 Evaluate side-chains 182 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 70 optimal weight: 0.0470 chunk 125 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 644 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099295 restraints weight = 24024.159| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.45 r_work: 0.3173 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15404 Z= 0.129 Angle : 0.522 10.226 21099 Z= 0.258 Chirality : 0.044 0.305 2612 Planarity : 0.003 0.036 2562 Dihedral : 6.733 96.647 3490 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.85 % Allowed : 8.68 % Favored : 89.47 % 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: 0.74 (0.21), residues: 1586 helix: 1.96 (0.28), residues: 367 sheet: 0.55 (0.24), residues: 432 loop : -0.19 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.013 0.001 TYR E 638 PHE 0.014 0.001 PHE A 53 TRP 0.014 0.001 TRP D 479 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00301 (15294) covalent geometry : angle 0.49461 (20804) SS BOND : bond 0.00378 ( 35) SS BOND : angle 1.04652 ( 70) hydrogen bonds : bond 0.03534 ( 451) hydrogen bonds : angle 4.42073 ( 1239) link_ALPHA1-3 : bond 0.01040 ( 2) link_ALPHA1-3 : angle 1.91576 ( 6) link_ALPHA1-6 : bond 0.01006 ( 2) link_ALPHA1-6 : angle 1.86090 ( 6) link_BETA1-4 : bond 0.00473 ( 16) link_BETA1-4 : angle 1.50738 ( 48) link_NAG-ASN : bond 0.00270 ( 55) link_NAG-ASN : angle 1.63506 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.514 Fit side-chains REVERT: A 363 GLN cc_start: 0.8508 (pm20) cc_final: 0.8134 (tp40) REVERT: A 479 TRP cc_start: 0.8086 (m-10) cc_final: 0.7466 (m-10) REVERT: B 634 GLU cc_start: 0.8295 (tt0) cc_final: 0.8039 (tt0) REVERT: C 100 MET cc_start: 0.9338 (mtp) cc_final: 0.9027 (mtp) REVERT: C 227 LYS cc_start: 0.8658 (ttpt) cc_final: 0.8321 (tttt) REVERT: E 629 MET cc_start: 0.9269 (mmm) cc_final: 0.8827 (mmm) REVERT: D 207 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7886 (tptt) REVERT: F 543 GLN cc_start: 0.8452 (mm-40) cc_final: 0.7700 (tm-30) REVERT: F 575 GLN cc_start: 0.7594 (mm-40) cc_final: 0.6940 (tp40) REVERT: F 588 LYS cc_start: 0.9246 (ttpp) cc_final: 0.9029 (ttpt) outliers start: 27 outliers final: 19 residues processed: 189 average time/residue: 0.1374 time to fit residues: 38.0829 Evaluate side-chains 181 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 131 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 644 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.125602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096152 restraints weight = 23995.185| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.43 r_work: 0.3120 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15404 Z= 0.200 Angle : 0.601 11.272 21099 Z= 0.295 Chirality : 0.046 0.313 2612 Planarity : 0.003 0.037 2562 Dihedral : 6.810 96.549 3490 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.71 % Allowed : 9.43 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.21), residues: 1586 helix: 1.85 (0.27), residues: 366 sheet: 0.23 (0.25), residues: 412 loop : -0.38 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 480 TYR 0.013 0.001 TYR A 217 PHE 0.022 0.002 PHE A 53 TRP 0.015 0.001 TRP A 69 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00480 (15294) covalent geometry : angle 0.57244 (20804) SS BOND : bond 0.00440 ( 35) SS BOND : angle 1.25113 ( 70) hydrogen bonds : bond 0.03955 ( 451) hydrogen bonds : angle 4.58054 ( 1239) link_ALPHA1-3 : bond 0.00942 ( 2) link_ALPHA1-3 : angle 1.88528 ( 6) link_ALPHA1-6 : bond 0.01013 ( 2) link_ALPHA1-6 : angle 1.87923 ( 6) link_BETA1-4 : bond 0.00509 ( 16) link_BETA1-4 : angle 1.63760 ( 48) link_NAG-ASN : bond 0.00335 ( 55) link_NAG-ASN : angle 1.79247 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 244 THR cc_start: 0.8610 (m) cc_final: 0.8409 (m) REVERT: A 479 TRP cc_start: 0.8116 (m-10) cc_final: 0.6990 (m-10) REVERT: B 634 GLU cc_start: 0.8203 (tt0) cc_final: 0.7956 (tt0) REVERT: C 227 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8310 (tttt) REVERT: C 246 GLN cc_start: 0.7786 (tp40) cc_final: 0.7525 (tp-100) REVERT: D 207 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7865 (tptt) REVERT: F 543 GLN cc_start: 0.8589 (mm-40) cc_final: 0.7962 (tm-30) REVERT: F 588 LYS cc_start: 0.9280 (ttpp) cc_final: 0.9028 (ttpt) outliers start: 25 outliers final: 21 residues processed: 184 average time/residue: 0.1381 time to fit residues: 36.8020 Evaluate side-chains 183 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 120 optimal weight: 0.0770 chunk 159 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 651 ASN F 575 GLN F 644 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.126787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097627 restraints weight = 23938.046| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.42 r_work: 0.3149 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15404 Z= 0.133 Angle : 0.537 9.904 21099 Z= 0.264 Chirality : 0.044 0.307 2612 Planarity : 0.003 0.039 2562 Dihedral : 6.522 94.786 3490 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.64 % Allowed : 9.84 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.21), residues: 1586 helix: 1.95 (0.28), residues: 366 sheet: 0.29 (0.25), residues: 413 loop : -0.45 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.012 0.001 TYR E 638 PHE 0.013 0.001 PHE D 53 TRP 0.014 0.001 TRP D 479 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00312 (15294) covalent geometry : angle 0.50917 (20804) SS BOND : bond 0.00390 ( 35) SS BOND : angle 1.04515 ( 70) hydrogen bonds : bond 0.03615 ( 451) hydrogen bonds : angle 4.40232 ( 1239) link_ALPHA1-3 : bond 0.01001 ( 2) link_ALPHA1-3 : angle 1.81082 ( 6) link_ALPHA1-6 : bond 0.01063 ( 2) link_ALPHA1-6 : angle 1.92733 ( 6) link_BETA1-4 : bond 0.00514 ( 16) link_BETA1-4 : angle 1.50158 ( 48) link_NAG-ASN : bond 0.00267 ( 55) link_NAG-ASN : angle 1.67056 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.6582 (mp0) cc_final: 0.6249 (pm20) REVERT: A 244 THR cc_start: 0.8547 (m) cc_final: 0.8327 (m) REVERT: A 479 TRP cc_start: 0.8055 (m-10) cc_final: 0.7011 (m-10) REVERT: B 634 GLU cc_start: 0.8197 (tt0) cc_final: 0.7928 (tt0) REVERT: C 100 MET cc_start: 0.9296 (mtp) cc_final: 0.9041 (mtp) REVERT: C 227 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8242 (tttt) REVERT: D 207 LYS cc_start: 0.8330 (mmtt) cc_final: 0.7842 (tptt) REVERT: F 543 GLN cc_start: 0.8464 (mm-40) cc_final: 0.7868 (tm-30) REVERT: F 575 GLN cc_start: 0.7712 (mm-40) cc_final: 0.6824 (tp40) outliers start: 24 outliers final: 20 residues processed: 182 average time/residue: 0.1412 time to fit residues: 37.3840 Evaluate side-chains 179 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 59 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 143 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.123700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.093949 restraints weight = 24246.960| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.54 r_work: 0.3070 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15404 Z= 0.253 Angle : 0.649 11.239 21099 Z= 0.317 Chirality : 0.048 0.315 2612 Planarity : 0.004 0.037 2562 Dihedral : 6.886 95.588 3490 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.85 % Allowed : 9.43 % Favored : 88.72 % 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: 0.09 (0.21), residues: 1586 helix: 1.53 (0.27), residues: 375 sheet: 0.00 (0.25), residues: 419 loop : -0.58 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 542 TYR 0.016 0.001 TYR C 217 PHE 0.016 0.002 PHE A 53 TRP 0.019 0.002 TRP D 112 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00606 (15294) covalent geometry : angle 0.61835 (20804) SS BOND : bond 0.00492 ( 35) SS BOND : angle 1.39179 ( 70) hydrogen bonds : bond 0.04208 ( 451) hydrogen bonds : angle 4.68344 ( 1239) link_ALPHA1-3 : bond 0.00834 ( 2) link_ALPHA1-3 : angle 1.77723 ( 6) link_ALPHA1-6 : bond 0.00967 ( 2) link_ALPHA1-6 : angle 1.91738 ( 6) link_BETA1-4 : bond 0.00485 ( 16) link_BETA1-4 : angle 1.70041 ( 48) link_NAG-ASN : bond 0.00386 ( 55) link_NAG-ASN : angle 1.91989 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.570 Fit side-chains REVERT: A 33 GLU cc_start: 0.6625 (mp0) cc_final: 0.6269 (pm20) REVERT: A 479 TRP cc_start: 0.8228 (m-10) cc_final: 0.7056 (m-10) REVERT: B 634 GLU cc_start: 0.8348 (tt0) cc_final: 0.8095 (tt0) REVERT: C 82 GLN cc_start: 0.8134 (pm20) cc_final: 0.7690 (pp30) REVERT: C 227 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8384 (tttt) REVERT: C 246 GLN cc_start: 0.7891 (tp-100) cc_final: 0.7621 (tp-100) REVERT: D 207 LYS cc_start: 0.8455 (mmtt) cc_final: 0.7480 (tptt) REVERT: F 542 ARG cc_start: 0.8767 (mtp85) cc_final: 0.8545 (mtp85) REVERT: F 543 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8016 (tm-30) outliers start: 27 outliers final: 23 residues processed: 179 average time/residue: 0.1364 time to fit residues: 35.8066 Evaluate side-chains 178 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 590 GLN F 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096585 restraints weight = 24313.459| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.41 r_work: 0.3121 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15404 Z= 0.149 Angle : 0.572 10.007 21099 Z= 0.282 Chirality : 0.045 0.310 2612 Planarity : 0.003 0.039 2562 Dihedral : 6.569 93.509 3490 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.44 % Allowed : 9.84 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.21), residues: 1586 helix: 1.78 (0.27), residues: 372 sheet: 0.09 (0.25), residues: 410 loop : -0.61 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 542 TYR 0.013 0.001 TYR E 638 PHE 0.014 0.001 PHE D 53 TRP 0.017 0.001 TRP A 69 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00352 (15294) covalent geometry : angle 0.54342 (20804) SS BOND : bond 0.00398 ( 35) SS BOND : angle 1.19651 ( 70) hydrogen bonds : bond 0.03729 ( 451) hydrogen bonds : angle 4.47916 ( 1239) link_ALPHA1-3 : bond 0.00930 ( 2) link_ALPHA1-3 : angle 1.72489 ( 6) link_ALPHA1-6 : bond 0.01032 ( 2) link_ALPHA1-6 : angle 1.93427 ( 6) link_BETA1-4 : bond 0.00511 ( 16) link_BETA1-4 : angle 1.54344 ( 48) link_NAG-ASN : bond 0.00268 ( 55) link_NAG-ASN : angle 1.74455 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.571 Fit side-chains REVERT: A 33 GLU cc_start: 0.6568 (mp0) cc_final: 0.6279 (pm20) REVERT: A 479 TRP cc_start: 0.8127 (m-10) cc_final: 0.7116 (m-10) REVERT: B 634 GLU cc_start: 0.8167 (tt0) cc_final: 0.7922 (tt0) REVERT: C 82 GLN cc_start: 0.8133 (pm20) cc_final: 0.7720 (pp30) REVERT: C 100 MET cc_start: 0.9300 (mtp) cc_final: 0.9041 (mtp) REVERT: C 227 LYS cc_start: 0.8603 (ttpt) cc_final: 0.8267 (tttt) REVERT: C 246 GLN cc_start: 0.7822 (tp-100) cc_final: 0.7602 (tp-100) REVERT: E 535 MET cc_start: 0.6831 (mmm) cc_final: 0.6248 (mtm) REVERT: D 207 LYS cc_start: 0.8438 (mmtt) cc_final: 0.7504 (tptt) REVERT: F 543 GLN cc_start: 0.8548 (mm-40) cc_final: 0.7985 (tm-30) outliers start: 21 outliers final: 20 residues processed: 179 average time/residue: 0.1409 time to fit residues: 36.7713 Evaluate side-chains 178 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 103 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 590 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 644 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097351 restraints weight = 24156.020| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.42 r_work: 0.3140 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15404 Z= 0.133 Angle : 0.550 9.689 21099 Z= 0.271 Chirality : 0.044 0.310 2612 Planarity : 0.003 0.037 2562 Dihedral : 6.233 90.714 3490 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.50 % Allowed : 9.84 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.29 (0.21), residues: 1586 helix: 1.98 (0.28), residues: 367 sheet: 0.18 (0.25), residues: 407 loop : -0.62 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.012 0.001 TYR E 638 PHE 0.013 0.001 PHE A 53 TRP 0.018 0.001 TRP A 69 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00315 (15294) covalent geometry : angle 0.52221 (20804) SS BOND : bond 0.00364 ( 35) SS BOND : angle 1.27797 ( 70) hydrogen bonds : bond 0.03540 ( 451) hydrogen bonds : angle 4.36952 ( 1239) link_ALPHA1-3 : bond 0.00945 ( 2) link_ALPHA1-3 : angle 1.67099 ( 6) link_ALPHA1-6 : bond 0.01015 ( 2) link_ALPHA1-6 : angle 1.81016 ( 6) link_BETA1-4 : bond 0.00515 ( 16) link_BETA1-4 : angle 1.51472 ( 48) link_NAG-ASN : bond 0.00261 ( 55) link_NAG-ASN : angle 1.66496 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.549 Fit side-chains REVERT: A 33 GLU cc_start: 0.6577 (mp0) cc_final: 0.6306 (pm20) REVERT: A 479 TRP cc_start: 0.8056 (m-10) cc_final: 0.7066 (m-10) REVERT: B 634 GLU cc_start: 0.8142 (tt0) cc_final: 0.7899 (tt0) REVERT: C 82 GLN cc_start: 0.8127 (pm20) cc_final: 0.7702 (pp30) REVERT: C 100 MET cc_start: 0.9282 (mtp) cc_final: 0.9046 (mtp) REVERT: C 227 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8253 (tttm) REVERT: E 535 MET cc_start: 0.6593 (mmm) cc_final: 0.6230 (mtp) REVERT: D 207 LYS cc_start: 0.8413 (mmtt) cc_final: 0.7891 (tptt) REVERT: D 432 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8314 (ptmm) REVERT: F 542 ARG cc_start: 0.8750 (mtp85) cc_final: 0.8194 (mtp85) REVERT: F 543 GLN cc_start: 0.8483 (mm-40) cc_final: 0.7900 (tm-30) REVERT: F 575 GLN cc_start: 0.7717 (mm-40) cc_final: 0.6858 (tp40) outliers start: 22 outliers final: 21 residues processed: 185 average time/residue: 0.1307 time to fit residues: 35.2362 Evaluate side-chains 185 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 58 optimal weight: 0.0170 chunk 110 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 590 GLN ** D 114 GLN ** 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 = 0.3681 r_free = 0.3681 target = 0.126238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097602 restraints weight = 24002.049| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.39 r_work: 0.3143 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15404 Z= 0.137 Angle : 0.556 10.019 21099 Z= 0.275 Chirality : 0.044 0.311 2612 Planarity : 0.003 0.042 2562 Dihedral : 5.882 88.355 3490 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.44 % Allowed : 9.71 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.31 (0.21), residues: 1586 helix: 1.99 (0.27), residues: 367 sheet: 0.20 (0.25), residues: 409 loop : -0.61 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.011 0.001 TYR E 638 PHE 0.014 0.001 PHE A 53 TRP 0.018 0.001 TRP A 69 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00323 (15294) covalent geometry : angle 0.52654 (20804) SS BOND : bond 0.00378 ( 35) SS BOND : angle 1.42250 ( 70) hydrogen bonds : bond 0.03537 ( 451) hydrogen bonds : angle 4.34954 ( 1239) link_ALPHA1-3 : bond 0.00909 ( 2) link_ALPHA1-3 : angle 1.53065 ( 6) link_ALPHA1-6 : bond 0.00889 ( 2) link_ALPHA1-6 : angle 1.81767 ( 6) link_BETA1-4 : bond 0.00511 ( 16) link_BETA1-4 : angle 1.51808 ( 48) link_NAG-ASN : bond 0.00264 ( 55) link_NAG-ASN : angle 1.68038 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4469.90 seconds wall clock time: 77 minutes 8.17 seconds (4628.17 seconds total)