Starting phenix.real_space_refine on Sun Aug 4 03:17:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcx_37113/08_2024/8kcx_37113.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcx_37113/08_2024/8kcx_37113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcx_37113/08_2024/8kcx_37113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcx_37113/08_2024/8kcx_37113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcx_37113/08_2024/8kcx_37113.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcx_37113/08_2024/8kcx_37113.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 56 5.16 5 C 6264 2.51 5 N 1456 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C ARG 127": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 524": "NH1" <-> "NH2" Residue "C GLU 555": "OE1" <-> "OE2" Residue "C ARG 780": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9486 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4608 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 550} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4608 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 550} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" 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: "F" 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: "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: "H" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 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: "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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.65, per 1000 atoms: 0.60 Number of scatterers: 9486 At special positions: 0 Unit cell: (95.865, 83.415, 128.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 56 16.00 O 1708 8.00 N 1456 7.00 C 6264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 479 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 782 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG E 1 " - " ASN A 83 " " NAG F 1 " - " ASN A 136 " " NAG G 1 " - " ASN A 67 " " NAG H 1 " - " ASN A 57 " " NAG I 1 " - " ASN C 83 " " NAG J 1 " - " ASN C 136 " " NAG K 1 " - " ASN C 67 " " NAG L 1 " - " ASN C 57 " Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 791 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 795 " pdb=" ZN C 901 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 791 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 563 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 795 " 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 48.5% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 302 through 335 removed outlier: 3.869A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS A 324 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 473 removed outlier: 3.855A pdb=" N ILE A 449 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 450 " --> pdb=" O TRP A 446 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Proline residue: A 458 - end of helix removed outlier: 3.565A pdb=" N GLN A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.873A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.774A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 528 removed outlier: 3.845A pdb=" N GLY A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 563 removed outlier: 3.558A pdb=" N GLY A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 575 removed outlier: 3.540A pdb=" N PHE A 571 " --> pdb=" O ASN A 567 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 575' Processing helix chain 'A' and resid 575 through 592 Processing helix chain 'A' and resid 606 through 615 removed outlier: 3.592A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.801A pdb=" N VAL A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 removed outlier: 3.741A pdb=" N SER A 633 " --> pdb=" O TRP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 649 removed outlier: 3.572A pdb=" N SER A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 735 removed outlier: 4.131A pdb=" N LEU A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 723 " --> pdb=" O CYS A 719 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR A 728 " --> pdb=" O TYR A 724 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 762 removed outlier: 3.558A pdb=" N CYS A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 789 through 811 removed outlier: 3.630A pdb=" N ALA A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 302 through 335 removed outlier: 3.869A pdb=" N TYR C 306 " --> pdb=" O LYS C 302 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE C 317 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 321 " --> pdb=" O PHE C 317 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE C 335 " --> pdb=" O HIS C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 473 removed outlier: 3.855A pdb=" N ILE C 449 " --> pdb=" O PHE C 445 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 450 " --> pdb=" O TRP C 446 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 451 " --> pdb=" O ASN C 447 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 452 " --> pdb=" O ILE C 448 " (cutoff:3.500A) Proline residue: C 458 - end of helix removed outlier: 3.565A pdb=" N GLN C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 465 " --> pdb=" O GLN C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 3.873A pdb=" N ALA C 486 " --> pdb=" O PHE C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 500 removed outlier: 3.774A pdb=" N ILE C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 528 removed outlier: 3.845A pdb=" N GLY C 508 " --> pdb=" O HIS C 504 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 509 " --> pdb=" O VAL C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 563 removed outlier: 3.558A pdb=" N GLY C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 575 removed outlier: 3.540A pdb=" N PHE C 571 " --> pdb=" O ASN C 567 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C 572 " --> pdb=" O TYR C 568 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 574 " --> pdb=" O ASN C 570 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C 575 " --> pdb=" O PHE C 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 567 through 575' Processing helix chain 'C' and resid 575 through 592 Processing helix chain 'C' and resid 606 through 615 removed outlier: 3.592A pdb=" N VAL C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 621 removed outlier: 3.801A pdb=" N VAL C 620 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 633 removed outlier: 3.741A pdb=" N SER C 633 " --> pdb=" O TRP C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 649 removed outlier: 3.572A pdb=" N SER C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C 645 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 647 " --> pdb=" O LEU C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 735 removed outlier: 4.131A pdb=" N LEU C 721 " --> pdb=" O PHE C 717 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C 723 " --> pdb=" O CYS C 719 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR C 728 " --> pdb=" O TYR C 724 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 729 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 730 " --> pdb=" O ALA C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 762 removed outlier: 3.558A pdb=" N CYS C 746 " --> pdb=" O VAL C 742 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE C 760 " --> pdb=" O ALA C 756 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 776 Processing helix chain 'C' and resid 777 through 779 No H-bonds generated for 'chain 'C' and resid 777 through 779' Processing helix chain 'C' and resid 789 through 811 removed outlier: 3.630A pdb=" N ALA C 799 " --> pdb=" O HIS C 795 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 4.809A pdb=" N ASN A 67 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.456A pdb=" N ALA A 77 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.856A pdb=" N ARG A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 46 removed outlier: 4.809A pdb=" N ASN C 67 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 51 through 56 removed outlier: 4.456A pdb=" N ALA C 77 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.856A pdb=" N ARG C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'C' and resid 187 through 192 488 hydrogen bonds defined for protein. 1398 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: 2.94 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2794 1.34 - 1.46: 2618 1.46 - 1.58: 4234 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 9732 Sorted by residual: bond pdb=" N ILE A 581 " pdb=" CA ILE A 581 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" N ILE C 581 " pdb=" CA ILE C 581 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" N ILE A 612 " pdb=" CA ILE A 612 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.27e+00 bond pdb=" N ILE C 612 " pdb=" CA ILE C 612 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.27e+00 bond pdb=" N MET A 152 " pdb=" CA MET A 152 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.16e-02 7.43e+03 7.03e+00 ... (remaining 9727 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.17: 278 107.17 - 113.91: 5510 113.91 - 120.65: 4070 120.65 - 127.39: 3288 127.39 - 134.13: 90 Bond angle restraints: 13236 Sorted by residual: angle pdb=" N LEU A 516 " pdb=" CA LEU A 516 " pdb=" C LEU A 516 " ideal model delta sigma weight residual 111.36 107.64 3.72 1.09e+00 8.42e-01 1.17e+01 angle pdb=" N LEU C 516 " pdb=" CA LEU C 516 " pdb=" C LEU C 516 " ideal model delta sigma weight residual 111.36 107.64 3.72 1.09e+00 8.42e-01 1.17e+01 angle pdb=" N THR C 575 " pdb=" CA THR C 575 " pdb=" C THR C 575 " ideal model delta sigma weight residual 113.12 109.07 4.05 1.25e+00 6.40e-01 1.05e+01 angle pdb=" N THR A 575 " pdb=" CA THR A 575 " pdb=" C THR A 575 " ideal model delta sigma weight residual 113.12 109.07 4.05 1.25e+00 6.40e-01 1.05e+01 angle pdb=" N ILE C 451 " pdb=" CA ILE C 451 " pdb=" C ILE C 451 " ideal model delta sigma weight residual 110.72 107.46 3.26 1.01e+00 9.80e-01 1.04e+01 ... (remaining 13231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 5264 21.51 - 43.02: 484 43.02 - 64.52: 74 64.52 - 86.03: 40 86.03 - 107.54: 48 Dihedral angle restraints: 5910 sinusoidal: 2520 harmonic: 3390 Sorted by residual: dihedral pdb=" CB CYS A 212 " pdb=" SG CYS A 212 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual 93.00 54.10 38.90 1 1.00e+01 1.00e-02 2.13e+01 dihedral pdb=" CB CYS C 212 " pdb=" SG CYS C 212 " pdb=" SG CYS C 271 " pdb=" CB CYS C 271 " ideal model delta sinusoidal sigma weight residual 93.00 54.10 38.90 1 1.00e+01 1.00e-02 2.13e+01 dihedral pdb=" CB CYS C 485 " pdb=" SG CYS C 485 " pdb=" SG CYS C 782 " pdb=" CB CYS C 782 " ideal model delta sinusoidal sigma weight residual 93.00 126.23 -33.23 1 1.00e+01 1.00e-02 1.57e+01 ... (remaining 5907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1228 0.057 - 0.114: 264 0.114 - 0.172: 64 0.172 - 0.229: 12 0.229 - 0.286: 6 Chirality restraints: 1574 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1571 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 182 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO C 183 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 182 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A 183 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 771 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO C 772 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 772 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 772 " -0.022 5.00e-02 4.00e+02 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2659 2.80 - 3.32: 7823 3.32 - 3.85: 15509 3.85 - 4.37: 17476 4.37 - 4.90: 30672 Nonbonded interactions: 74139 Sorted by model distance: nonbonded pdb=" OG SER A 59 " pdb=" O3 NAG H 1 " model vdw 2.273 3.040 nonbonded pdb=" OG SER C 59 " pdb=" O3 NAG L 1 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASN A 447 " pdb=" CD1 LEU C 587 " model vdw 2.292 3.460 nonbonded pdb=" CD1 LEU A 587 " pdb=" OD1 ASN C 447 " model vdw 2.292 3.460 nonbonded pdb=" OH TYR C 210 " pdb=" O GLY C 272 " model vdw 2.294 3.040 ... (remaining 74134 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' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' } 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: 0.390 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 30.430 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 0.058 9732 Z= 0.334 Angle : 0.769 10.121 13236 Z= 0.434 Chirality : 0.055 0.286 1574 Planarity : 0.004 0.050 1604 Dihedral : 20.462 107.539 3694 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.39 % Allowed : 19.02 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.22), residues: 1114 helix: -3.03 (0.15), residues: 498 sheet: 1.43 (0.30), residues: 270 loop : -1.68 (0.27), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 106 HIS 0.007 0.001 HIS A 504 PHE 0.012 0.001 PHE C 454 TYR 0.016 0.001 TYR C 724 ARG 0.002 0.000 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 282 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LYS cc_start: 0.9196 (pttt) cc_final: 0.8989 (pttp) REVERT: A 256 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8336 (mp0) REVERT: A 265 LYS cc_start: 0.9253 (mttm) cc_final: 0.8920 (mtpt) REVERT: A 446 TRP cc_start: 0.8147 (t60) cc_final: 0.7544 (t-100) REVERT: A 451 ILE cc_start: 0.8639 (mt) cc_final: 0.8288 (mp) REVERT: A 550 ILE cc_start: 0.9272 (mm) cc_final: 0.9037 (mm) REVERT: A 713 MET cc_start: 0.9041 (tpp) cc_final: 0.8838 (tpt) REVERT: A 721 LEU cc_start: 0.8898 (tt) cc_final: 0.8515 (mt) REVERT: A 754 TRP cc_start: 0.9348 (m100) cc_final: 0.9077 (m100) REVERT: A 774 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8589 (mt-10) REVERT: C 251 LYS cc_start: 0.9196 (pttt) cc_final: 0.8990 (pttp) REVERT: C 256 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8336 (mp0) REVERT: C 265 LYS cc_start: 0.9256 (mttm) cc_final: 0.8922 (mtpt) REVERT: C 446 TRP cc_start: 0.8149 (t60) cc_final: 0.7544 (t-100) REVERT: C 451 ILE cc_start: 0.8639 (mt) cc_final: 0.8289 (mp) REVERT: C 550 ILE cc_start: 0.9271 (mm) cc_final: 0.9035 (mm) REVERT: C 713 MET cc_start: 0.9042 (tpp) cc_final: 0.8837 (tpt) REVERT: C 721 LEU cc_start: 0.8900 (tt) cc_final: 0.8516 (mt) REVERT: C 754 TRP cc_start: 0.9345 (m100) cc_final: 0.9075 (m100) REVERT: C 774 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8588 (mt-10) outliers start: 4 outliers final: 2 residues processed: 282 average time/residue: 0.8670 time to fit residues: 266.9938 Evaluate side-chains 212 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 210 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain C residue 579 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN C 467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9732 Z= 0.254 Angle : 0.643 9.197 13236 Z= 0.315 Chirality : 0.046 0.270 1574 Planarity : 0.004 0.037 1604 Dihedral : 14.537 82.555 1644 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.20 % Allowed : 20.10 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1114 helix: -0.67 (0.21), residues: 490 sheet: 1.20 (0.30), residues: 270 loop : -1.48 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 106 HIS 0.005 0.001 HIS C 504 PHE 0.012 0.001 PHE A 608 TYR 0.013 0.001 TYR A 724 ARG 0.005 0.001 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 240 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8506 (mp10) cc_final: 0.8282 (mm-40) REVERT: A 256 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8329 (mp0) REVERT: A 265 LYS cc_start: 0.9348 (mttm) cc_final: 0.9038 (mtpt) REVERT: A 334 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.5816 (tpm170) REVERT: A 446 TRP cc_start: 0.8104 (OUTLIER) cc_final: 0.7608 (t-100) REVERT: A 554 MET cc_start: 0.8660 (tpp) cc_final: 0.8285 (tpp) REVERT: A 559 SER cc_start: 0.9072 (m) cc_final: 0.8730 (t) REVERT: A 713 MET cc_start: 0.8960 (tpp) cc_final: 0.8585 (tpt) REVERT: A 737 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: A 774 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8743 (mt-10) REVERT: C 123 GLN cc_start: 0.8508 (mp10) cc_final: 0.8281 (mm-40) REVERT: C 256 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8328 (mp0) REVERT: C 265 LYS cc_start: 0.9349 (mttm) cc_final: 0.9038 (mtpt) REVERT: C 334 ARG cc_start: 0.6397 (OUTLIER) cc_final: 0.5820 (tpm170) REVERT: C 446 TRP cc_start: 0.8104 (OUTLIER) cc_final: 0.7607 (t-100) REVERT: C 554 MET cc_start: 0.8662 (tpp) cc_final: 0.8286 (tpp) REVERT: C 559 SER cc_start: 0.9074 (m) cc_final: 0.8730 (t) REVERT: C 713 MET cc_start: 0.8961 (tpp) cc_final: 0.8584 (tpt) REVERT: C 737 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: C 774 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8743 (mt-10) outliers start: 53 outliers final: 26 residues processed: 266 average time/residue: 0.8714 time to fit residues: 253.4669 Evaluate side-chains 250 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 732 LYS Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 786 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN C 467 GLN C 570 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9732 Z= 0.344 Angle : 0.626 8.101 13236 Z= 0.306 Chirality : 0.047 0.290 1574 Planarity : 0.003 0.035 1604 Dihedral : 10.815 69.883 1640 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 5.59 % Allowed : 22.45 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1114 helix: 0.49 (0.23), residues: 490 sheet: 1.17 (0.30), residues: 270 loop : -1.39 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 106 HIS 0.004 0.001 HIS C 522 PHE 0.026 0.001 PHE A 312 TYR 0.014 0.001 TYR C 568 ARG 0.004 0.000 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 210 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8717 (mp10) cc_final: 0.8477 (mm-40) REVERT: A 256 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8303 (mp0) REVERT: A 265 LYS cc_start: 0.9376 (mttm) cc_final: 0.9000 (mtpt) REVERT: A 302 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7953 (mmmt) REVERT: A 334 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.5994 (tpm170) REVERT: A 446 TRP cc_start: 0.8146 (OUTLIER) cc_final: 0.7876 (t-100) REVERT: A 554 MET cc_start: 0.8625 (tpp) cc_final: 0.8206 (tpp) REVERT: A 559 SER cc_start: 0.9093 (m) cc_final: 0.8784 (t) REVERT: A 713 MET cc_start: 0.8919 (tpp) cc_final: 0.8590 (tpt) REVERT: A 718 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8129 (mp) REVERT: A 754 TRP cc_start: 0.9220 (m100) cc_final: 0.9008 (m100) REVERT: A 774 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8761 (mt-10) REVERT: C 123 GLN cc_start: 0.8716 (mp10) cc_final: 0.8480 (mm-40) REVERT: C 256 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8301 (mp0) REVERT: C 265 LYS cc_start: 0.9375 (mttm) cc_final: 0.8999 (mtpt) REVERT: C 302 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.7955 (mmmt) REVERT: C 334 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.5995 (tpm170) REVERT: C 446 TRP cc_start: 0.8147 (OUTLIER) cc_final: 0.7878 (t-100) REVERT: C 554 MET cc_start: 0.8627 (tpp) cc_final: 0.8207 (tpp) REVERT: C 559 SER cc_start: 0.9094 (m) cc_final: 0.8784 (t) REVERT: C 713 MET cc_start: 0.8919 (tpp) cc_final: 0.8590 (tpt) REVERT: C 718 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8130 (mp) REVERT: C 754 TRP cc_start: 0.9219 (m100) cc_final: 0.9008 (m100) REVERT: C 774 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8760 (mt-10) outliers start: 57 outliers final: 30 residues processed: 238 average time/residue: 0.8061 time to fit residues: 211.3265 Evaluate side-chains 250 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 212 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 786 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 467 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN C 121 ASN C 467 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9732 Z= 0.191 Angle : 0.562 9.148 13236 Z= 0.269 Chirality : 0.044 0.268 1574 Planarity : 0.003 0.033 1604 Dihedral : 8.256 57.113 1640 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 5.49 % Allowed : 23.53 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1114 helix: 0.97 (0.23), residues: 490 sheet: 1.23 (0.29), residues: 270 loop : -1.23 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.002 0.001 HIS A 229 PHE 0.013 0.001 PHE A 509 TYR 0.017 0.001 TYR A 568 ARG 0.003 0.000 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 226 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8674 (mp10) cc_final: 0.8468 (mm-40) REVERT: A 205 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8944 (m) REVERT: A 256 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8323 (mp0) REVERT: A 265 LYS cc_start: 0.9368 (mttm) cc_final: 0.9004 (mtpt) REVERT: A 302 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7907 (mmmt) REVERT: A 306 TYR cc_start: 0.9234 (m-80) cc_final: 0.9000 (m-80) REVERT: A 334 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.5788 (tpm170) REVERT: A 446 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.7643 (t-100) REVERT: A 542 PHE cc_start: 0.8044 (m-10) cc_final: 0.7750 (m-10) REVERT: A 559 SER cc_start: 0.9077 (m) cc_final: 0.8800 (t) REVERT: A 572 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8460 (mp10) REVERT: A 608 PHE cc_start: 0.4891 (OUTLIER) cc_final: 0.3499 (m-80) REVERT: A 643 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.7032 (mm) REVERT: A 713 MET cc_start: 0.8895 (tpp) cc_final: 0.8565 (tpt) REVERT: A 718 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 754 TRP cc_start: 0.9217 (m100) cc_final: 0.8942 (m100) REVERT: A 774 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8738 (mt-10) REVERT: A 783 ILE cc_start: 0.8894 (pp) cc_final: 0.8657 (pp) REVERT: C 123 GLN cc_start: 0.8672 (mp10) cc_final: 0.8465 (mm-40) REVERT: C 205 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8944 (m) REVERT: C 256 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8323 (mp0) REVERT: C 265 LYS cc_start: 0.9366 (mttm) cc_final: 0.9002 (mtpt) REVERT: C 302 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7912 (mmmt) REVERT: C 306 TYR cc_start: 0.9234 (m-80) cc_final: 0.9000 (m-80) REVERT: C 334 ARG cc_start: 0.6275 (OUTLIER) cc_final: 0.5789 (tpm170) REVERT: C 446 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.7642 (t-100) REVERT: C 542 PHE cc_start: 0.8040 (m-10) cc_final: 0.7750 (m-10) REVERT: C 559 SER cc_start: 0.9078 (m) cc_final: 0.8800 (t) REVERT: C 572 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8456 (mp10) REVERT: C 608 PHE cc_start: 0.4895 (OUTLIER) cc_final: 0.3502 (m-80) REVERT: C 643 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.7038 (mm) REVERT: C 713 MET cc_start: 0.8895 (tpp) cc_final: 0.8564 (tpt) REVERT: C 718 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8093 (mp) REVERT: C 754 TRP cc_start: 0.9218 (m100) cc_final: 0.8943 (m100) REVERT: C 774 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8737 (mt-10) REVERT: C 783 ILE cc_start: 0.8896 (pp) cc_final: 0.8659 (pp) outliers start: 56 outliers final: 28 residues processed: 266 average time/residue: 0.7927 time to fit residues: 232.7423 Evaluate side-chains 258 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 214 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 467 GLN Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 572 GLN Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 786 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 567 ASN C 467 GLN C 567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 9732 Z= 0.577 Angle : 0.690 8.785 13236 Z= 0.343 Chirality : 0.050 0.293 1574 Planarity : 0.004 0.035 1604 Dihedral : 7.621 57.021 1640 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 7.25 % Allowed : 23.33 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1114 helix: 0.96 (0.23), residues: 490 sheet: 1.16 (0.30), residues: 268 loop : -1.27 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 106 HIS 0.007 0.001 HIS C 522 PHE 0.017 0.002 PHE C 312 TYR 0.016 0.002 TYR C 188 ARG 0.004 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 210 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8575 (mp0) cc_final: 0.8131 (tp30) REVERT: A 256 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8289 (mp0) REVERT: A 265 LYS cc_start: 0.9391 (mttm) cc_final: 0.9061 (mtpt) REVERT: A 302 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.7977 (mmmt) REVERT: A 306 TYR cc_start: 0.9340 (m-80) cc_final: 0.9064 (m-80) REVERT: A 334 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.5784 (tpm170) REVERT: A 446 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.7940 (t-100) REVERT: A 554 MET cc_start: 0.8561 (tpp) cc_final: 0.8251 (tpp) REVERT: A 559 SER cc_start: 0.9108 (m) cc_final: 0.8810 (t) REVERT: A 608 PHE cc_start: 0.5020 (OUTLIER) cc_final: 0.3643 (m-80) REVERT: A 713 MET cc_start: 0.8923 (tpp) cc_final: 0.8563 (tpt) REVERT: A 718 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 737 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: A 754 TRP cc_start: 0.9284 (m100) cc_final: 0.9047 (m100) REVERT: A 774 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8816 (mt-10) REVERT: A 790 ASP cc_start: 0.9070 (m-30) cc_final: 0.8745 (m-30) REVERT: C 124 GLU cc_start: 0.8571 (mp0) cc_final: 0.8129 (tp30) REVERT: C 256 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8288 (mp0) REVERT: C 265 LYS cc_start: 0.9390 (mttm) cc_final: 0.9061 (mtpt) REVERT: C 302 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.7980 (mmmt) REVERT: C 306 TYR cc_start: 0.9339 (m-80) cc_final: 0.9065 (m-80) REVERT: C 334 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5786 (tpm170) REVERT: C 446 TRP cc_start: 0.8198 (OUTLIER) cc_final: 0.7939 (t-100) REVERT: C 554 MET cc_start: 0.8559 (tpp) cc_final: 0.8251 (tpp) REVERT: C 559 SER cc_start: 0.9110 (m) cc_final: 0.8812 (t) REVERT: C 608 PHE cc_start: 0.5022 (OUTLIER) cc_final: 0.3644 (m-80) REVERT: C 713 MET cc_start: 0.8923 (tpp) cc_final: 0.8561 (tpt) REVERT: C 718 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8195 (mp) REVERT: C 737 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: C 754 TRP cc_start: 0.9284 (m100) cc_final: 0.9047 (m100) REVERT: C 774 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8816 (mt-10) REVERT: C 790 ASP cc_start: 0.9071 (m-30) cc_final: 0.8747 (m-30) outliers start: 74 outliers final: 40 residues processed: 256 average time/residue: 0.7647 time to fit residues: 216.5239 Evaluate side-chains 261 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 209 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 793 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN C 467 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9732 Z= 0.219 Angle : 0.570 9.081 13236 Z= 0.278 Chirality : 0.044 0.258 1574 Planarity : 0.003 0.035 1604 Dihedral : 6.615 50.130 1640 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.69 % Allowed : 24.51 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1114 helix: 1.27 (0.23), residues: 490 sheet: 1.26 (0.29), residues: 268 loop : -1.25 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 106 HIS 0.002 0.001 HIS C 229 PHE 0.016 0.001 PHE C 509 TYR 0.024 0.001 TYR C 568 ARG 0.004 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 218 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8305 (mp0) REVERT: A 265 LYS cc_start: 0.9362 (mttm) cc_final: 0.9035 (mtpt) REVERT: A 302 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.7918 (mmmt) REVERT: A 306 TYR cc_start: 0.9174 (m-80) cc_final: 0.8869 (m-80) REVERT: A 334 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.5749 (tpm170) REVERT: A 542 PHE cc_start: 0.7985 (m-10) cc_final: 0.7630 (m-10) REVERT: A 554 MET cc_start: 0.8456 (tpp) cc_final: 0.8134 (tpp) REVERT: A 559 SER cc_start: 0.9060 (m) cc_final: 0.8776 (t) REVERT: A 567 ASN cc_start: 0.8804 (t0) cc_final: 0.8282 (t0) REVERT: A 572 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8511 (mp10) REVERT: A 608 PHE cc_start: 0.4956 (OUTLIER) cc_final: 0.3662 (m-80) REVERT: A 713 MET cc_start: 0.8949 (tpp) cc_final: 0.8626 (tpt) REVERT: A 718 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8057 (mp) REVERT: A 737 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: A 754 TRP cc_start: 0.9256 (m100) cc_final: 0.8905 (m100) REVERT: A 774 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8757 (mt-10) REVERT: C 256 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8302 (mp0) REVERT: C 265 LYS cc_start: 0.9361 (mttm) cc_final: 0.9034 (mtpt) REVERT: C 302 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.7922 (mmmt) REVERT: C 306 TYR cc_start: 0.9175 (m-80) cc_final: 0.8870 (m-80) REVERT: C 334 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5751 (tpm170) REVERT: C 446 TRP cc_start: 0.8119 (OUTLIER) cc_final: 0.7730 (t-100) REVERT: C 542 PHE cc_start: 0.7982 (m-10) cc_final: 0.7628 (m-10) REVERT: C 554 MET cc_start: 0.8463 (tpp) cc_final: 0.8136 (tpp) REVERT: C 559 SER cc_start: 0.9091 (m) cc_final: 0.8814 (t) REVERT: C 567 ASN cc_start: 0.8803 (t0) cc_final: 0.8274 (t0) REVERT: C 572 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8517 (mp10) REVERT: C 608 PHE cc_start: 0.4959 (OUTLIER) cc_final: 0.3665 (m-80) REVERT: C 713 MET cc_start: 0.8950 (tpp) cc_final: 0.8626 (tpt) REVERT: C 718 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8055 (mp) REVERT: C 737 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: C 754 TRP cc_start: 0.9257 (m100) cc_final: 0.8905 (m100) REVERT: C 774 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8757 (mt-10) outliers start: 58 outliers final: 32 residues processed: 254 average time/residue: 0.8009 time to fit residues: 223.8721 Evaluate side-chains 263 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 218 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 572 GLN Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 786 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0870 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 572 GLN C 467 GLN C 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9732 Z= 0.178 Angle : 0.559 9.329 13236 Z= 0.273 Chirality : 0.044 0.256 1574 Planarity : 0.003 0.033 1604 Dihedral : 6.037 50.633 1640 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 5.88 % Allowed : 24.71 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1114 helix: 1.38 (0.23), residues: 502 sheet: 1.31 (0.29), residues: 270 loop : -1.20 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 106 HIS 0.002 0.001 HIS C 229 PHE 0.007 0.001 PHE C 573 TYR 0.013 0.001 TYR C 188 ARG 0.004 0.000 ARG C 523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 228 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8305 (mp0) REVERT: A 265 LYS cc_start: 0.9369 (mttm) cc_final: 0.9037 (mtpt) REVERT: A 302 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7882 (mmmt) REVERT: A 306 TYR cc_start: 0.9141 (m-80) cc_final: 0.8866 (m-80) REVERT: A 334 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5694 (tpm170) REVERT: A 446 TRP cc_start: 0.8028 (t60) cc_final: 0.7788 (t-100) REVERT: A 542 PHE cc_start: 0.7972 (m-10) cc_final: 0.7698 (m-10) REVERT: A 554 MET cc_start: 0.8453 (tpp) cc_final: 0.8134 (tpp) REVERT: A 559 SER cc_start: 0.9053 (m) cc_final: 0.8783 (t) REVERT: A 572 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8537 (mp10) REVERT: A 608 PHE cc_start: 0.4835 (OUTLIER) cc_final: 0.3517 (m-80) REVERT: A 713 MET cc_start: 0.8941 (tpp) cc_final: 0.8629 (tpt) REVERT: A 718 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8072 (mp) REVERT: A 732 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8130 (mppt) REVERT: A 737 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: A 774 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8762 (mt-10) REVERT: C 256 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8303 (mp0) REVERT: C 265 LYS cc_start: 0.9368 (mttm) cc_final: 0.9036 (mtpt) REVERT: C 302 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7884 (mmmt) REVERT: C 306 TYR cc_start: 0.9141 (m-80) cc_final: 0.8866 (m-80) REVERT: C 334 ARG cc_start: 0.6275 (OUTLIER) cc_final: 0.5696 (tpm170) REVERT: C 446 TRP cc_start: 0.8098 (OUTLIER) cc_final: 0.7718 (t-100) REVERT: C 542 PHE cc_start: 0.7972 (m-10) cc_final: 0.7699 (m-10) REVERT: C 554 MET cc_start: 0.8459 (tpp) cc_final: 0.8139 (tpp) REVERT: C 559 SER cc_start: 0.9053 (m) cc_final: 0.8782 (t) REVERT: C 572 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8507 (mp10) REVERT: C 608 PHE cc_start: 0.4838 (OUTLIER) cc_final: 0.3518 (m-80) REVERT: C 713 MET cc_start: 0.8942 (tpp) cc_final: 0.8629 (tpt) REVERT: C 718 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8071 (mp) REVERT: C 732 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8130 (mppt) REVERT: C 737 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: C 774 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8768 (mt-10) outliers start: 60 outliers final: 28 residues processed: 272 average time/residue: 0.8323 time to fit residues: 248.3943 Evaluate side-chains 269 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 572 GLN Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 732 LYS Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 793 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 467 GLN A 475 ASN A 567 ASN A 572 GLN A 764 ASN C 467 GLN C 475 ASN C 567 ASN C 572 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9732 Z= 0.261 Angle : 0.597 9.439 13236 Z= 0.293 Chirality : 0.045 0.259 1574 Planarity : 0.003 0.033 1604 Dihedral : 5.795 50.261 1640 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 5.98 % Allowed : 25.10 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1114 helix: 1.41 (0.23), residues: 502 sheet: 1.26 (0.29), residues: 270 loop : -1.18 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 106 HIS 0.004 0.001 HIS A 504 PHE 0.016 0.001 PHE A 509 TYR 0.025 0.001 TYR A 568 ARG 0.004 0.000 ARG C 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 228 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8301 (mp0) REVERT: A 265 LYS cc_start: 0.9378 (mttm) cc_final: 0.9044 (mtpt) REVERT: A 302 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7874 (mmmt) REVERT: A 306 TYR cc_start: 0.9153 (m-80) cc_final: 0.8852 (m-80) REVERT: A 334 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.5700 (tpm170) REVERT: A 446 TRP cc_start: 0.8106 (t60) cc_final: 0.7863 (t-100) REVERT: A 542 PHE cc_start: 0.8034 (m-10) cc_final: 0.7708 (m-10) REVERT: A 554 MET cc_start: 0.8470 (tpp) cc_final: 0.8167 (tpp) REVERT: A 559 SER cc_start: 0.9052 (m) cc_final: 0.8794 (t) REVERT: A 572 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8563 (mp10) REVERT: A 608 PHE cc_start: 0.4905 (OUTLIER) cc_final: 0.3589 (m-80) REVERT: A 713 MET cc_start: 0.8938 (tpp) cc_final: 0.8627 (tpt) REVERT: A 732 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8129 (mppt) REVERT: A 737 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: A 774 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8746 (mt-10) REVERT: C 256 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8301 (mp0) REVERT: C 265 LYS cc_start: 0.9377 (mttm) cc_final: 0.9042 (mtpt) REVERT: C 302 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7877 (mmmt) REVERT: C 306 TYR cc_start: 0.9153 (m-80) cc_final: 0.8852 (m-80) REVERT: C 334 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5701 (tpm170) REVERT: C 542 PHE cc_start: 0.8033 (m-10) cc_final: 0.7707 (m-10) REVERT: C 554 MET cc_start: 0.8473 (tpp) cc_final: 0.8172 (tpp) REVERT: C 559 SER cc_start: 0.9054 (m) cc_final: 0.8797 (t) REVERT: C 567 ASN cc_start: 0.8761 (t0) cc_final: 0.8314 (t0) REVERT: C 572 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8503 (mp10) REVERT: C 608 PHE cc_start: 0.4902 (OUTLIER) cc_final: 0.3577 (m-80) REVERT: C 713 MET cc_start: 0.8938 (tpp) cc_final: 0.8627 (tpt) REVERT: C 732 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8126 (mppt) REVERT: C 737 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: C 774 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8747 (mt-10) outliers start: 61 outliers final: 37 residues processed: 266 average time/residue: 0.8917 time to fit residues: 259.6470 Evaluate side-chains 277 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 228 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 572 GLN Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 732 LYS Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 793 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 0.0870 chunk 66 optimal weight: 5.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 475 ASN A 572 GLN C 467 GLN C 475 ASN C 572 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9732 Z= 0.253 Angle : 0.598 9.543 13236 Z= 0.294 Chirality : 0.045 0.256 1574 Planarity : 0.003 0.033 1604 Dihedral : 5.622 50.336 1640 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 5.20 % Allowed : 25.98 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1114 helix: 1.51 (0.23), residues: 502 sheet: 1.29 (0.29), residues: 270 loop : -1.17 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.004 0.001 HIS A 504 PHE 0.015 0.001 PHE A 509 TYR 0.014 0.001 TYR C 188 ARG 0.004 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 222 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8300 (mp0) REVERT: A 265 LYS cc_start: 0.9377 (mttm) cc_final: 0.9045 (mtpt) REVERT: A 302 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7861 (mmmt) REVERT: A 306 TYR cc_start: 0.9154 (m-80) cc_final: 0.8848 (m-80) REVERT: A 334 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5700 (tpm170) REVERT: A 446 TRP cc_start: 0.8144 (t60) cc_final: 0.7894 (t-100) REVERT: A 509 PHE cc_start: 0.8830 (t80) cc_final: 0.8625 (t80) REVERT: A 542 PHE cc_start: 0.8038 (m-10) cc_final: 0.7720 (m-10) REVERT: A 554 MET cc_start: 0.8462 (tpp) cc_final: 0.8126 (tpp) REVERT: A 559 SER cc_start: 0.9050 (m) cc_final: 0.8798 (t) REVERT: A 567 ASN cc_start: 0.8690 (t0) cc_final: 0.8218 (t0) REVERT: A 572 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8459 (mp10) REVERT: A 608 PHE cc_start: 0.4939 (OUTLIER) cc_final: 0.3580 (m-80) REVERT: A 713 MET cc_start: 0.8942 (tpp) cc_final: 0.8738 (tpt) REVERT: A 732 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8130 (mppt) REVERT: A 737 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: A 774 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8743 (mt-10) REVERT: A 792 ASP cc_start: 0.8985 (m-30) cc_final: 0.8701 (m-30) REVERT: C 256 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8299 (mp0) REVERT: C 265 LYS cc_start: 0.9375 (mttm) cc_final: 0.9044 (mtpt) REVERT: C 302 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7866 (mmmt) REVERT: C 306 TYR cc_start: 0.9154 (m-80) cc_final: 0.8848 (m-80) REVERT: C 334 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.5700 (tpm170) REVERT: C 446 TRP cc_start: 0.8135 (t60) cc_final: 0.7883 (t-100) REVERT: C 509 PHE cc_start: 0.8830 (t80) cc_final: 0.8626 (t80) REVERT: C 542 PHE cc_start: 0.8036 (m-10) cc_final: 0.7721 (m-10) REVERT: C 554 MET cc_start: 0.8466 (tpp) cc_final: 0.8131 (tpp) REVERT: C 559 SER cc_start: 0.9052 (m) cc_final: 0.8798 (t) REVERT: C 567 ASN cc_start: 0.8760 (t0) cc_final: 0.8306 (t0) REVERT: C 572 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8470 (mp10) REVERT: C 608 PHE cc_start: 0.4940 (OUTLIER) cc_final: 0.3583 (m-80) REVERT: C 713 MET cc_start: 0.8943 (tpp) cc_final: 0.8738 (tpt) REVERT: C 732 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8127 (mppt) REVERT: C 737 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: C 774 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8742 (mt-10) REVERT: C 792 ASP cc_start: 0.8990 (m-30) cc_final: 0.8706 (m-30) outliers start: 53 outliers final: 35 residues processed: 256 average time/residue: 0.8985 time to fit residues: 251.3064 Evaluate side-chains 267 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 220 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 467 GLN Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 572 GLN Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 732 LYS Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 793 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 113 optimal weight: 0.3980 chunk 104 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 572 GLN C 467 GLN C 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9732 Z= 0.178 Angle : 0.592 9.713 13236 Z= 0.291 Chirality : 0.044 0.248 1574 Planarity : 0.003 0.032 1604 Dihedral : 5.446 50.643 1640 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.71 % Allowed : 26.67 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1114 helix: 1.63 (0.23), residues: 502 sheet: 1.35 (0.29), residues: 270 loop : -1.14 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 106 HIS 0.004 0.001 HIS C 504 PHE 0.015 0.001 PHE A 571 TYR 0.024 0.001 TYR C 568 ARG 0.004 0.000 ARG A 523 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 234 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7765 (p0) REVERT: A 256 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8299 (mp0) REVERT: A 265 LYS cc_start: 0.9369 (mttm) cc_final: 0.9044 (mtpt) REVERT: A 302 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7845 (mmmt) REVERT: A 306 TYR cc_start: 0.9077 (m-80) cc_final: 0.8763 (m-80) REVERT: A 334 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.5636 (tpm170) REVERT: A 446 TRP cc_start: 0.8029 (t60) cc_final: 0.7813 (t-100) REVERT: A 509 PHE cc_start: 0.8827 (t80) cc_final: 0.8620 (t80) REVERT: A 542 PHE cc_start: 0.7993 (m-10) cc_final: 0.7673 (m-10) REVERT: A 554 MET cc_start: 0.8435 (tpp) cc_final: 0.8108 (tpp) REVERT: A 559 SER cc_start: 0.9037 (m) cc_final: 0.8800 (t) REVERT: A 567 ASN cc_start: 0.8656 (t0) cc_final: 0.8196 (t0) REVERT: A 608 PHE cc_start: 0.5278 (OUTLIER) cc_final: 0.3885 (m-80) REVERT: A 732 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8141 (mppt) REVERT: A 737 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: A 774 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8741 (mt-10) REVERT: A 783 ILE cc_start: 0.8866 (pp) cc_final: 0.8617 (pp) REVERT: A 792 ASP cc_start: 0.8910 (m-30) cc_final: 0.8609 (m-30) REVERT: C 73 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7763 (p0) REVERT: C 256 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8298 (mp0) REVERT: C 265 LYS cc_start: 0.9367 (mttm) cc_final: 0.9042 (mtpt) REVERT: C 302 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7850 (mmmt) REVERT: C 306 TYR cc_start: 0.9078 (m-80) cc_final: 0.8763 (m-80) REVERT: C 334 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5638 (tpm170) REVERT: C 446 TRP cc_start: 0.8009 (t60) cc_final: 0.7791 (t-100) REVERT: C 509 PHE cc_start: 0.8827 (t80) cc_final: 0.8623 (t80) REVERT: C 542 PHE cc_start: 0.7993 (m-10) cc_final: 0.7675 (m-10) REVERT: C 554 MET cc_start: 0.8439 (tpp) cc_final: 0.8097 (tpp) REVERT: C 559 SER cc_start: 0.9039 (m) cc_final: 0.8800 (t) REVERT: C 608 PHE cc_start: 0.5278 (OUTLIER) cc_final: 0.3889 (m-80) REVERT: C 732 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8137 (mppt) REVERT: C 737 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: C 774 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8742 (mt-10) REVERT: C 792 ASP cc_start: 0.8912 (m-30) cc_final: 0.8617 (m-30) outliers start: 48 outliers final: 30 residues processed: 266 average time/residue: 0.8639 time to fit residues: 251.2211 Evaluate side-chains 273 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 231 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 732 LYS Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 793 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 475 ASN C 467 GLN C 475 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.095052 restraints weight = 12393.468| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.85 r_work: 0.2929 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9732 Z= 0.205 Angle : 0.602 9.673 13236 Z= 0.296 Chirality : 0.044 0.252 1574 Planarity : 0.003 0.032 1604 Dihedral : 5.264 50.465 1640 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.61 % Allowed : 26.57 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.24), residues: 1114 helix: 1.73 (0.22), residues: 502 sheet: 1.38 (0.29), residues: 270 loop : -1.14 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.005 0.001 HIS C 504 PHE 0.014 0.001 PHE A 509 TYR 0.013 0.001 TYR A 188 ARG 0.005 0.000 ARG A 523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3975.41 seconds wall clock time: 70 minutes 7.64 seconds (4207.64 seconds total)