Starting phenix.real_space_refine on Sat Jul 20 01:48:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcx_37113/07_2024/8kcx_37113_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcx_37113/07_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_37113/07_2024/8kcx_37113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcx_37113/07_2024/8kcx_37113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcx_37113/07_2024/8kcx_37113_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kcx_37113/07_2024/8kcx_37113_neut.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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.68, 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: 4.36 Conformation dependent library (CDL) restraints added in 1.7 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: 0.99 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: 2.79 Time building geometry restraints manager: 4.75 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 2.440 nonbonded pdb=" OG SER C 59 " pdb=" O3 NAG L 1 " model vdw 2.273 2.440 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 2.440 ... (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 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: 0.490 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 31.170 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.310 ------------------------------------------------------------------------------- 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 : 0.995 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: 0.8651 time to fit residues: 266.3234 Evaluate side-chains 212 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 210 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 0.6980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 467 GLN C 143 GLN C 467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9732 Z= 0.177 Angle : 0.597 8.126 13236 Z= 0.292 Chirality : 0.045 0.276 1574 Planarity : 0.004 0.038 1604 Dihedral : 15.402 89.309 1644 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.41 % Allowed : 22.06 % Favored : 73.53 % 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: -0.80 (0.22), residues: 1114 helix: -0.79 (0.20), residues: 500 sheet: 1.24 (0.30), residues: 270 loop : -1.40 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 106 HIS 0.003 0.001 HIS C 504 PHE 0.011 0.001 PHE C 545 TYR 0.012 0.001 TYR C 188 ARG 0.004 0.000 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 283 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 238 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8560 (mp10) cc_final: 0.8336 (mm-40) REVERT: A 188 TYR cc_start: 0.9290 (p90) cc_final: 0.9081 (p90) REVERT: A 256 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8334 (mp0) REVERT: A 265 LYS cc_start: 0.9263 (mttm) cc_final: 0.8957 (mtpt) REVERT: A 334 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.5926 (tpm170) REVERT: A 446 TRP cc_start: 0.8081 (OUTLIER) cc_final: 0.7592 (t-100) REVERT: A 554 MET cc_start: 0.8613 (tpp) cc_final: 0.8242 (tpp) REVERT: A 559 SER cc_start: 0.9078 (m) cc_final: 0.8738 (t) REVERT: A 713 MET cc_start: 0.8952 (tpp) cc_final: 0.8703 (tpt) REVERT: A 737 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: A 774 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8668 (mt-10) REVERT: C 123 GLN cc_start: 0.8558 (mp10) cc_final: 0.8336 (mm-40) REVERT: C 188 TYR cc_start: 0.9291 (p90) cc_final: 0.9082 (p90) REVERT: C 256 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8335 (mp0) REVERT: C 265 LYS cc_start: 0.9264 (mttm) cc_final: 0.8958 (mtpt) REVERT: C 334 ARG cc_start: 0.6533 (OUTLIER) cc_final: 0.5926 (tpm170) REVERT: C 446 TRP cc_start: 0.8084 (OUTLIER) cc_final: 0.7594 (t-100) REVERT: C 554 MET cc_start: 0.8614 (tpp) cc_final: 0.8240 (tpp) REVERT: C 559 SER cc_start: 0.9081 (m) cc_final: 0.8739 (t) REVERT: C 713 MET cc_start: 0.8953 (tpp) cc_final: 0.8703 (tpt) REVERT: C 737 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: C 774 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8666 (mt-10) outliers start: 45 outliers final: 16 residues processed: 254 average time/residue: 0.8474 time to fit residues: 235.5367 Evaluate side-chains 238 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 216 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 716 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 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 716 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: 0.6980 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 475 ASN A 570 ASN C 99 GLN C 475 ASN C 570 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9732 Z= 0.417 Angle : 0.645 8.230 13236 Z= 0.317 Chirality : 0.048 0.302 1574 Planarity : 0.003 0.035 1604 Dihedral : 11.195 76.720 1640 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 6.57 % Allowed : 23.63 % 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: 0.09 (0.23), residues: 1114 helix: 0.47 (0.23), residues: 488 sheet: 1.22 (0.30), residues: 268 loop : -1.37 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 754 HIS 0.009 0.001 HIS C 504 PHE 0.019 0.001 PHE C 312 TYR 0.013 0.001 TYR C 188 ARG 0.003 0.000 ARG C 523 *********************** 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 286 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 219 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8325 (mp0) REVERT: A 265 LYS cc_start: 0.9269 (mttm) cc_final: 0.8958 (mtpt) REVERT: A 302 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.7954 (mmmt) REVERT: A 334 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.5883 (tpm170) REVERT: A 446 TRP cc_start: 0.8181 (OUTLIER) cc_final: 0.7926 (t-100) REVERT: A 554 MET cc_start: 0.8700 (tpp) cc_final: 0.8337 (tpp) REVERT: A 559 SER cc_start: 0.9101 (m) cc_final: 0.8783 (t) REVERT: A 713 MET cc_start: 0.8933 (tpp) cc_final: 0.8586 (tpt) REVERT: A 718 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8230 (mp) REVERT: A 774 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8818 (mt-10) REVERT: C 256 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8323 (mp0) REVERT: C 265 LYS cc_start: 0.9269 (mttm) cc_final: 0.8959 (mtpt) REVERT: C 302 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.7955 (mmmt) REVERT: C 334 ARG cc_start: 0.6388 (OUTLIER) cc_final: 0.5885 (tpm170) REVERT: C 446 TRP cc_start: 0.8183 (OUTLIER) cc_final: 0.7927 (t-100) REVERT: C 554 MET cc_start: 0.8698 (tpp) cc_final: 0.8334 (tpp) REVERT: C 559 SER cc_start: 0.9103 (m) cc_final: 0.8783 (t) REVERT: C 713 MET cc_start: 0.8934 (tpp) cc_final: 0.8587 (tpt) REVERT: C 718 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8231 (mp) REVERT: C 774 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8818 (mt-10) outliers start: 67 outliers final: 32 residues processed: 257 average time/residue: 0.8711 time to fit residues: 244.8762 Evaluate side-chains 249 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 209 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 148 ASP 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 307 VAL 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 557 VAL Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 718 ILE 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 A residue 800 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 ASP 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 307 VAL 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 557 VAL Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 800 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 467 GLN A 475 ASN A 572 GLN C 121 ASN C 467 GLN C 475 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9732 Z= 0.177 Angle : 0.541 8.801 13236 Z= 0.262 Chirality : 0.044 0.266 1574 Planarity : 0.003 0.037 1604 Dihedral : 8.825 63.669 1640 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 5.49 % Allowed : 25.10 % 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: 0.54 (0.24), residues: 1114 helix: 0.99 (0.23), residues: 488 sheet: 1.24 (0.30), residues: 270 loop : -1.20 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 106 HIS 0.004 0.001 HIS C 504 PHE 0.006 0.001 PHE A 258 TYR 0.017 0.001 TYR A 568 ARG 0.003 0.000 ARG A 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 276 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 220 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8321 (mp0) REVERT: A 265 LYS cc_start: 0.9274 (mttm) cc_final: 0.8967 (mtpt) REVERT: A 302 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.7896 (mmmt) REVERT: A 334 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5790 (tpm170) REVERT: A 446 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7655 (t-100) REVERT: A 554 MET cc_start: 0.8658 (tpp) cc_final: 0.8213 (tpp) REVERT: A 559 SER cc_start: 0.9091 (m) cc_final: 0.8788 (t) REVERT: A 572 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8503 (mp10) REVERT: A 608 PHE cc_start: 0.4871 (OUTLIER) cc_final: 0.3483 (m-80) REVERT: A 643 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7185 (mm) REVERT: A 713 MET cc_start: 0.8948 (tpp) cc_final: 0.8597 (tpt) REVERT: A 718 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8176 (mp) REVERT: A 737 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: A 774 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8741 (mt-10) REVERT: C 256 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8315 (mp0) REVERT: C 265 LYS cc_start: 0.9276 (mttm) cc_final: 0.8969 (mtpt) REVERT: C 302 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.7898 (mmmt) REVERT: C 334 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5792 (tpm170) REVERT: C 446 TRP cc_start: 0.8101 (OUTLIER) cc_final: 0.7655 (t-100) REVERT: C 554 MET cc_start: 0.8660 (tpp) cc_final: 0.8213 (tpp) REVERT: C 559 SER cc_start: 0.9093 (m) cc_final: 0.8788 (t) REVERT: C 572 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8507 (mp10) REVERT: C 608 PHE cc_start: 0.4874 (OUTLIER) cc_final: 0.3485 (m-80) REVERT: C 643 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7187 (mm) REVERT: C 713 MET cc_start: 0.8948 (tpp) cc_final: 0.8597 (tpt) REVERT: C 718 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8178 (mp) REVERT: C 737 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: C 774 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8741 (mt-10) outliers start: 56 outliers final: 20 residues processed: 252 average time/residue: 0.8555 time to fit residues: 236.3566 Evaluate side-chains 254 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 218 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 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 643 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 737 GLU 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 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 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 643 LEU Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 737 GLU 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: 4.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 9732 Z= 0.517 Angle : 0.649 8.933 13236 Z= 0.321 Chirality : 0.049 0.292 1574 Planarity : 0.003 0.037 1604 Dihedral : 8.056 54.963 1640 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 6.47 % Allowed : 25.00 % Favored : 68.53 % 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: 0.63 (0.24), residues: 1114 helix: 1.11 (0.23), residues: 488 sheet: 1.27 (0.30), residues: 266 loop : -1.18 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 106 HIS 0.006 0.001 HIS A 522 PHE 0.017 0.002 PHE A 312 TYR 0.015 0.001 TYR C 188 ARG 0.004 0.001 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 286 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 220 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8311 (mp0) REVERT: A 265 LYS cc_start: 0.9280 (mttm) cc_final: 0.8971 (mtpt) REVERT: A 302 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.7931 (mmmt) REVERT: A 334 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5781 (tpm170) REVERT: A 446 TRP cc_start: 0.8196 (OUTLIER) cc_final: 0.7963 (t-100) REVERT: A 554 MET cc_start: 0.8689 (tpp) cc_final: 0.8251 (tpp) REVERT: A 559 SER cc_start: 0.9097 (m) cc_final: 0.8798 (t) REVERT: A 567 ASN cc_start: 0.8783 (t0) cc_final: 0.8408 (t0) REVERT: A 572 GLN cc_start: 0.8832 (mp10) cc_final: 0.8574 (mp10) REVERT: A 608 PHE cc_start: 0.4993 (OUTLIER) cc_final: 0.3616 (m-80) REVERT: A 713 MET cc_start: 0.8925 (tpp) cc_final: 0.8566 (tpt) REVERT: A 718 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8158 (mp) REVERT: A 737 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: A 774 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8763 (mt-10) REVERT: A 790 ASP cc_start: 0.9068 (m-30) cc_final: 0.8714 (m-30) REVERT: C 256 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8310 (mp0) REVERT: C 265 LYS cc_start: 0.9280 (mttm) cc_final: 0.8972 (mtpt) REVERT: C 302 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.7937 (mmmt) REVERT: C 334 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.5782 (tpm170) REVERT: C 446 TRP cc_start: 0.8196 (OUTLIER) cc_final: 0.7963 (t-100) REVERT: C 554 MET cc_start: 0.8688 (tpp) cc_final: 0.8251 (tpp) REVERT: C 559 SER cc_start: 0.9099 (m) cc_final: 0.8800 (t) REVERT: C 567 ASN cc_start: 0.8781 (t0) cc_final: 0.8405 (t0) REVERT: C 572 GLN cc_start: 0.8833 (mp10) cc_final: 0.8575 (mp10) REVERT: C 608 PHE cc_start: 0.4992 (OUTLIER) cc_final: 0.3617 (m-80) REVERT: C 713 MET cc_start: 0.8926 (tpp) cc_final: 0.8566 (tpt) REVERT: C 718 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8158 (mp) REVERT: C 737 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: C 774 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8765 (mt-10) REVERT: C 790 ASP cc_start: 0.9068 (m-30) cc_final: 0.8715 (m-30) outliers start: 66 outliers final: 40 residues processed: 264 average time/residue: 0.8019 time to fit residues: 232.5056 Evaluate side-chains 265 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 213 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 148 ASP 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 462 LEU 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 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 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 A residue 814 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 ASP 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 462 LEU 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 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 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 Chi-restraints excluded: chain C residue 814 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 570 ASN A 572 GLN C 467 GLN C 475 ASN C 570 ASN C 572 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9732 Z= 0.300 Angle : 0.586 9.067 13236 Z= 0.287 Chirality : 0.045 0.268 1574 Planarity : 0.003 0.036 1604 Dihedral : 7.620 59.746 1640 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 6.67 % Allowed : 25.49 % Favored : 67.84 % 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: 0.73 (0.24), residues: 1114 helix: 1.20 (0.23), residues: 488 sheet: 1.31 (0.30), residues: 266 loop : -1.14 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.004 0.001 HIS A 504 PHE 0.009 0.001 PHE C 258 TYR 0.020 0.001 TYR A 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 274 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 206 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8309 (mp0) REVERT: A 265 LYS cc_start: 0.9290 (mttm) cc_final: 0.8990 (mtpt) REVERT: A 302 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7904 (mmmt) REVERT: A 334 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5768 (tpm170) REVERT: A 446 TRP cc_start: 0.8152 (OUTLIER) cc_final: 0.7764 (t-100) REVERT: A 554 MET cc_start: 0.8657 (tpp) cc_final: 0.8231 (tpp) REVERT: A 559 SER cc_start: 0.9114 (m) cc_final: 0.8804 (t) REVERT: A 567 ASN cc_start: 0.8764 (t0) cc_final: 0.8404 (t0) REVERT: A 572 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8457 (mp10) REVERT: A 608 PHE cc_start: 0.4976 (OUTLIER) cc_final: 0.3637 (m-80) REVERT: A 713 MET cc_start: 0.8926 (tpp) cc_final: 0.8553 (tpt) REVERT: A 737 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: A 774 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8750 (mt-10) REVERT: A 783 ILE cc_start: 0.9108 (pp) cc_final: 0.8903 (pp) REVERT: C 256 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8307 (mp0) REVERT: C 265 LYS cc_start: 0.9290 (mttm) cc_final: 0.8991 (mtpt) REVERT: C 302 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.7907 (mmmt) REVERT: C 334 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.5768 (tpm170) REVERT: C 446 TRP cc_start: 0.8158 (OUTLIER) cc_final: 0.7746 (t-100) REVERT: C 554 MET cc_start: 0.8656 (tpp) cc_final: 0.8226 (tpp) REVERT: C 559 SER cc_start: 0.9116 (m) cc_final: 0.8805 (t) REVERT: C 567 ASN cc_start: 0.8761 (t0) cc_final: 0.8400 (t0) REVERT: C 572 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8456 (mp10) REVERT: C 608 PHE cc_start: 0.4976 (OUTLIER) cc_final: 0.3637 (m-80) REVERT: C 713 MET cc_start: 0.8927 (tpp) cc_final: 0.8552 (tpt) REVERT: C 737 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: C 774 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8680 (mt-10) REVERT: C 783 ILE cc_start: 0.9116 (pp) cc_final: 0.8911 (pp) outliers start: 68 outliers final: 37 residues processed: 245 average time/residue: 0.8511 time to fit residues: 228.4722 Evaluate side-chains 251 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 202 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 148 ASP 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 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 498 ILE 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 608 PHE Chi-restraints excluded: chain A residue 716 ILE 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 148 ASP 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 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 498 ILE 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 584 LEU Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 716 ILE 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: 0.7980 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.7996 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9732 Z= 0.334 Angle : 0.595 9.185 13236 Z= 0.292 Chirality : 0.045 0.271 1574 Planarity : 0.003 0.036 1604 Dihedral : 7.054 54.608 1640 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 6.57 % Allowed : 25.29 % Favored : 68.14 % 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: 0.83 (0.24), residues: 1114 helix: 1.31 (0.23), residues: 488 sheet: 1.34 (0.30), residues: 266 loop : -1.11 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.004 0.001 HIS C 504 PHE 0.021 0.001 PHE C 509 TYR 0.015 0.001 TYR A 188 ARG 0.003 0.000 ARG A 518 *********************** 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 281 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 214 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8308 (mp0) REVERT: A 265 LYS cc_start: 0.9299 (mttm) cc_final: 0.9004 (mtpt) REVERT: A 302 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.7894 (mmmt) REVERT: A 334 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.5760 (tpm170) REVERT: A 554 MET cc_start: 0.8659 (tpp) cc_final: 0.8196 (tpp) REVERT: A 559 SER cc_start: 0.9115 (m) cc_final: 0.8809 (t) REVERT: A 567 ASN cc_start: 0.8758 (t0) cc_final: 0.8391 (t0) REVERT: A 572 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8374 (mp10) REVERT: A 578 MET cc_start: 0.7550 (mmp) cc_final: 0.7137 (mmm) REVERT: A 608 PHE cc_start: 0.4992 (OUTLIER) cc_final: 0.3681 (m-80) REVERT: A 713 MET cc_start: 0.8933 (tpp) cc_final: 0.8574 (tpt) REVERT: A 737 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: A 774 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8698 (mt-10) REVERT: A 783 ILE cc_start: 0.9133 (pp) cc_final: 0.8902 (pp) REVERT: C 256 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8304 (mp0) REVERT: C 265 LYS cc_start: 0.9299 (mttm) cc_final: 0.9006 (mtpt) REVERT: C 302 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.7898 (mmmt) REVERT: C 334 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.5763 (tpm170) REVERT: C 554 MET cc_start: 0.8657 (tpp) cc_final: 0.8195 (tpp) REVERT: C 559 SER cc_start: 0.9115 (m) cc_final: 0.8808 (t) REVERT: C 567 ASN cc_start: 0.8758 (t0) cc_final: 0.8389 (t0) REVERT: C 572 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8374 (mp10) REVERT: C 578 MET cc_start: 0.7552 (mmp) cc_final: 0.7139 (mmm) REVERT: C 608 PHE cc_start: 0.4995 (OUTLIER) cc_final: 0.3684 (m-80) REVERT: C 713 MET cc_start: 0.8933 (tpp) cc_final: 0.8572 (tpt) REVERT: C 737 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: C 774 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8699 (mt-10) REVERT: C 783 ILE cc_start: 0.9139 (pp) cc_final: 0.8879 (pp) outliers start: 67 outliers final: 42 residues processed: 253 average time/residue: 0.8296 time to fit residues: 230.2023 Evaluate side-chains 263 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 211 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 148 ASP 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 334 ARG Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 504 HIS 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 608 PHE Chi-restraints excluded: chain A residue 645 THR 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 814 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 148 ASP 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 334 ARG Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 504 HIS 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 608 PHE Chi-restraints excluded: chain C residue 645 THR 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 814 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9732 Z= 0.226 Angle : 0.585 9.477 13236 Z= 0.281 Chirality : 0.044 0.263 1574 Planarity : 0.003 0.035 1604 Dihedral : 6.434 50.241 1640 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.49 % Allowed : 26.67 % Favored : 67.84 % 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: 1.00 (0.24), residues: 1114 helix: 1.50 (0.23), residues: 488 sheet: 1.35 (0.29), residues: 266 loop : -1.05 (0.30), residues: 360 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 0.009 0.001 PHE A 571 TYR 0.022 0.001 TYR C 568 ARG 0.003 0.000 ARG A 518 *********************** 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 268 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 212 time to evaluate : 1.077 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: 0.8852 (mt-10) cc_final: 0.8425 (mp0) REVERT: A 265 LYS cc_start: 0.9285 (mttm) cc_final: 0.8993 (mtpt) REVERT: A 302 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7871 (mmmt) REVERT: A 334 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.5673 (tpm170) REVERT: A 446 TRP cc_start: 0.8139 (t60) cc_final: 0.7926 (t-100) REVERT: A 554 MET cc_start: 0.8641 (tpp) cc_final: 0.8216 (tpp) REVERT: A 559 SER cc_start: 0.9078 (m) cc_final: 0.8771 (t) REVERT: A 567 ASN cc_start: 0.8717 (t0) cc_final: 0.8357 (t0) REVERT: A 578 MET cc_start: 0.7544 (mmp) cc_final: 0.7110 (mmm) REVERT: A 608 PHE cc_start: 0.4851 (OUTLIER) cc_final: 0.3526 (m-80) REVERT: A 713 MET cc_start: 0.8929 (tpp) cc_final: 0.8564 (tpt) REVERT: A 737 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: A 774 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8694 (mt-10) REVERT: A 783 ILE cc_start: 0.9077 (pp) cc_final: 0.8768 (pp) REVERT: C 256 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8422 (mp0) REVERT: C 265 LYS cc_start: 0.9285 (mttm) cc_final: 0.8993 (mtpt) REVERT: C 302 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7876 (mmmt) REVERT: C 334 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.5675 (tpm170) REVERT: C 446 TRP cc_start: 0.8141 (t60) cc_final: 0.7920 (t-100) REVERT: C 554 MET cc_start: 0.8641 (tpp) cc_final: 0.8173 (tpp) REVERT: C 559 SER cc_start: 0.9078 (m) cc_final: 0.8772 (t) REVERT: C 567 ASN cc_start: 0.8714 (t0) cc_final: 0.8355 (t0) REVERT: C 578 MET cc_start: 0.7546 (mmp) cc_final: 0.7113 (mmm) REVERT: C 608 PHE cc_start: 0.4853 (OUTLIER) cc_final: 0.3527 (m-80) REVERT: C 713 MET cc_start: 0.8930 (tpp) cc_final: 0.8563 (tpt) REVERT: C 737 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: C 774 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8701 (mt-10) REVERT: C 783 ILE cc_start: 0.9084 (pp) cc_final: 0.8769 (pp) outliers start: 56 outliers final: 32 residues processed: 247 average time/residue: 0.9006 time to fit residues: 243.1777 Evaluate side-chains 247 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 148 ASP 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 334 ARG Chi-restraints excluded: chain A residue 462 LEU 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 737 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 814 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 148 ASP 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 334 ARG Chi-restraints excluded: chain C residue 462 LEU 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 737 GLU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 814 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 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 178 HIS A 467 GLN A 475 ASN A 570 ASN C 178 HIS C 467 GLN C 475 ASN C 570 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9732 Z= 0.339 Angle : 0.616 9.383 13236 Z= 0.300 Chirality : 0.046 0.276 1574 Planarity : 0.003 0.034 1604 Dihedral : 5.778 50.395 1640 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.88 % Allowed : 26.76 % Favored : 67.35 % 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: 1.05 (0.24), residues: 1114 helix: 1.53 (0.23), residues: 488 sheet: 1.38 (0.29), residues: 266 loop : -1.01 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 106 HIS 0.004 0.001 HIS C 504 PHE 0.026 0.001 PHE C 509 TYR 0.024 0.001 TYR C 568 ARG 0.003 0.000 ARG C 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 271 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 211 time to evaluate : 0.975 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: 0.8857 (mt-10) cc_final: 0.8426 (mp0) REVERT: A 265 LYS cc_start: 0.9302 (mttm) cc_final: 0.9007 (mtpt) REVERT: A 302 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7879 (mmmt) REVERT: A 322 LEU cc_start: 0.8675 (tp) cc_final: 0.8360 (tt) REVERT: A 334 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.5715 (tpm170) REVERT: A 446 TRP cc_start: 0.8187 (t60) cc_final: 0.7936 (t-100) REVERT: A 554 MET cc_start: 0.8657 (tpp) cc_final: 0.8205 (tpp) REVERT: A 555 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8189 (tm-30) REVERT: A 559 SER cc_start: 0.9083 (m) cc_final: 0.8775 (t) REVERT: A 567 ASN cc_start: 0.8703 (t0) cc_final: 0.8336 (t0) REVERT: A 572 GLN cc_start: 0.8792 (mp-120) cc_final: 0.8546 (mp10) REVERT: A 578 MET cc_start: 0.7557 (mmp) cc_final: 0.7111 (mmm) REVERT: A 608 PHE cc_start: 0.5057 (OUTLIER) cc_final: 0.3688 (m-80) REVERT: A 713 MET cc_start: 0.8913 (tpp) cc_final: 0.8535 (tpt) REVERT: A 737 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: A 774 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8688 (mt-10) REVERT: A 783 ILE cc_start: 0.9151 (pp) cc_final: 0.8893 (pp) REVERT: C 256 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8305 (mp0) REVERT: C 265 LYS cc_start: 0.9278 (mttm) cc_final: 0.8985 (mtpt) REVERT: C 302 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7884 (mmmt) REVERT: C 322 LEU cc_start: 0.8676 (tp) cc_final: 0.8362 (tt) REVERT: C 334 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.5716 (tpm170) REVERT: C 446 TRP cc_start: 0.8189 (t60) cc_final: 0.7931 (t-100) REVERT: C 554 MET cc_start: 0.8663 (tpp) cc_final: 0.8209 (tpp) REVERT: C 555 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8189 (tm-30) REVERT: C 559 SER cc_start: 0.9081 (m) cc_final: 0.8774 (t) REVERT: C 567 ASN cc_start: 0.8700 (t0) cc_final: 0.8334 (t0) REVERT: C 572 GLN cc_start: 0.8792 (mp-120) cc_final: 0.8546 (mp10) REVERT: C 578 MET cc_start: 0.7560 (mmp) cc_final: 0.7115 (mmm) REVERT: C 608 PHE cc_start: 0.5058 (OUTLIER) cc_final: 0.3689 (m-80) REVERT: C 713 MET cc_start: 0.8913 (tpp) cc_final: 0.8535 (tpt) REVERT: C 737 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: C 774 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8687 (mt-10) REVERT: C 783 ILE cc_start: 0.9166 (pp) cc_final: 0.8899 (pp) outliers start: 60 outliers final: 40 residues processed: 247 average time/residue: 0.8741 time to fit residues: 236.0059 Evaluate side-chains 257 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 209 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 148 ASP 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 310 SER 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 608 PHE Chi-restraints excluded: chain A residue 645 THR 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 A residue 814 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 148 ASP 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 310 SER 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 608 PHE Chi-restraints excluded: chain C residue 645 THR 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 Chi-restraints excluded: chain C residue 814 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.0010 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 113 GLN C 467 GLN C 475 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9732 Z= 0.170 Angle : 0.574 9.775 13236 Z= 0.279 Chirality : 0.044 0.258 1574 Planarity : 0.003 0.035 1604 Dihedral : 5.468 50.583 1640 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 4.12 % Allowed : 28.73 % Favored : 67.16 % 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: 1.21 (0.24), residues: 1114 helix: 1.70 (0.23), residues: 500 sheet: 1.36 (0.29), residues: 268 loop : -1.01 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.003 0.001 HIS C 504 PHE 0.006 0.001 PHE C 258 TYR 0.021 0.001 TYR C 568 ARG 0.003 0.000 ARG A 518 ********************** 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 259 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 217 time to evaluate : 1.248 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: 0.8850 (mt-10) cc_final: 0.8411 (mp0) REVERT: A 265 LYS cc_start: 0.9286 (mttm) cc_final: 0.8991 (mtpt) REVERT: A 302 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7835 (mmmt) REVERT: A 334 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.5695 (tpm170) REVERT: A 446 TRP cc_start: 0.8148 (t60) cc_final: 0.7926 (t-100) REVERT: A 554 MET cc_start: 0.8637 (tpp) cc_final: 0.8163 (tpp) REVERT: A 555 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8193 (tm-30) REVERT: A 559 SER cc_start: 0.9068 (m) cc_final: 0.8774 (t) REVERT: A 572 GLN cc_start: 0.8788 (mp-120) cc_final: 0.8559 (mp10) REVERT: A 578 MET cc_start: 0.7527 (mmp) cc_final: 0.7085 (mmm) REVERT: A 608 PHE cc_start: 0.5271 (OUTLIER) cc_final: 0.3941 (m-80) REVERT: A 713 MET cc_start: 0.8941 (tpp) cc_final: 0.8604 (tpt) REVERT: A 737 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: A 774 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8704 (mt-10) REVERT: A 783 ILE cc_start: 0.9048 (pp) cc_final: 0.8730 (pp) REVERT: C 256 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8411 (mp0) REVERT: C 265 LYS cc_start: 0.9261 (mttm) cc_final: 0.8971 (mtpt) REVERT: C 302 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7839 (mmmt) REVERT: C 334 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5697 (tpm170) REVERT: C 446 TRP cc_start: 0.8148 (t60) cc_final: 0.7920 (t-100) REVERT: C 554 MET cc_start: 0.8640 (tpp) cc_final: 0.8165 (tpp) REVERT: C 555 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8192 (tm-30) REVERT: C 559 SER cc_start: 0.9068 (m) cc_final: 0.8773 (t) REVERT: C 572 GLN cc_start: 0.8791 (mp-120) cc_final: 0.8560 (mp10) REVERT: C 578 MET cc_start: 0.7526 (mmp) cc_final: 0.7087 (mmm) REVERT: C 608 PHE cc_start: 0.5271 (OUTLIER) cc_final: 0.3941 (m-80) REVERT: C 713 MET cc_start: 0.8952 (tpp) cc_final: 0.8613 (tpt) REVERT: C 737 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: C 774 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8704 (mt-10) REVERT: C 783 ILE cc_start: 0.9059 (pp) cc_final: 0.8731 (pp) outliers start: 42 outliers final: 28 residues processed: 245 average time/residue: 0.8700 time to fit residues: 233.5903 Evaluate side-chains 253 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 217 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 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 608 PHE Chi-restraints excluded: chain A residue 645 THR 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 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 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 608 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 786 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 567 ASN C 467 GLN C 475 ASN C 567 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093838 restraints weight = 12395.328| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.86 r_work: 0.2901 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9732 Z= 0.247 Angle : 0.585 9.531 13236 Z= 0.287 Chirality : 0.044 0.274 1574 Planarity : 0.003 0.034 1604 Dihedral : 5.247 50.065 1640 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.22 % Allowed : 28.92 % Favored : 66.86 % 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: 1.24 (0.24), residues: 1114 helix: 1.74 (0.23), residues: 500 sheet: 1.42 (0.29), residues: 268 loop : -1.05 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 106 HIS 0.004 0.001 HIS A 504 PHE 0.027 0.001 PHE A 509 TYR 0.014 0.001 TYR A 188 ARG 0.003 0.000 ARG A 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3978.39 seconds wall clock time: 70 minutes 12.08 seconds (4212.08 seconds total)