Starting phenix.real_space_refine on Thu Feb 15 02:35:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3w_36863/02_2024/8k3w_36863.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3w_36863/02_2024/8k3w_36863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3w_36863/02_2024/8k3w_36863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3w_36863/02_2024/8k3w_36863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3w_36863/02_2024/8k3w_36863.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3w_36863/02_2024/8k3w_36863.pdb" } resolution = 2.91 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 7143 2.51 5 N 1753 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 488": "OD1" <-> "OD2" Residue "B ASP 500": "OD1" <-> "OD2" Residue "B TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B ASP 610": "OD1" <-> "OD2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 653": "OE1" <-> "OE2" Residue "B ASP 661": "OD1" <-> "OD2" Residue "B PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 703": "OE1" <-> "OE2" Residue "B GLU 723": "OE1" <-> "OE2" Residue "B TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 862": "OE1" <-> "OE2" Residue "B TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1060": "OE1" <-> "OE2" Residue "B GLU 1086": "OE1" <-> "OE2" Residue "B TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A ASP 610": "OD1" <-> "OD2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A ASP 661": "OD1" <-> "OD2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1060": "OE1" <-> "OE2" Residue "A GLU 1086": "OE1" <-> "OE2" Residue "A TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10916 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5360 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 20, 'TRANS': 673} Chain breaks: 5 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "A" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5380 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 20, 'TRANS': 673} Chain breaks: 5 Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 151 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {' MG': 1, 'POV': 1, 'UD1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {' MG': 1, 'POV': 1, 'UD1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 6.31, per 1000 atoms: 0.58 Number of scatterers: 10916 At special positions: 0 Unit cell: (125.19, 97.37, 114.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 6 15.00 Mg 2 11.99 O 1944 8.00 N 1753 7.00 C 7143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 2.1 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 6 sheets defined 64.0% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 410 through 413 removed outlier: 3.611A pdb=" N PHE B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.863A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 460 through 479 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 577 through 588 Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.554A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 618 through 621 removed outlier: 4.033A pdb=" N ASN B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 636 through 643 removed outlier: 5.909A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 669 removed outlier: 3.633A pdb=" N SER B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 662 " --> pdb=" O ASN B 658 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 716 through 726 removed outlier: 3.579A pdb=" N LEU B 720 " --> pdb=" O GLU B 716 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 4.091A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.564A pdb=" N SER B 781 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 removed outlier: 3.529A pdb=" N PHE B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 828 removed outlier: 3.737A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 856 removed outlier: 3.554A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 894 removed outlier: 3.957A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 932 Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.550A pdb=" N SER B 941 " --> pdb=" O HIS B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 948 Processing helix chain 'B' and resid 949 through 955 Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 998 through 1012 removed outlier: 3.741A pdb=" N GLN B1002 " --> pdb=" O SER B 998 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B1005 " --> pdb=" O ILE B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1060 Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1091 through 1127 removed outlier: 4.201A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 410 through 413 removed outlier: 3.611A pdb=" N PHE A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.863A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 458 through 478 removed outlier: 3.847A pdb=" N LEU A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.554A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 618 through 621 removed outlier: 4.033A pdb=" N ASN A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 621' Processing helix chain 'A' and resid 636 through 643 removed outlier: 5.909A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 669 removed outlier: 3.632A pdb=" N SER A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 711 through 714 Processing helix chain 'A' and resid 715 through 726 removed outlier: 3.797A pdb=" N LEU A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 4.091A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.564A pdb=" N SER A 781 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 removed outlier: 3.529A pdb=" N PHE A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.738A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.555A pdb=" N LEU A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 894 removed outlier: 3.958A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 932 Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.550A pdb=" N SER A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 949 through 955 Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 998 through 1012 removed outlier: 3.891A pdb=" N GLN A1002 " --> pdb=" O SER A 998 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A1005 " --> pdb=" O ILE A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1060 Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1091 through 1127 removed outlier: 4.201A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 386 through 390 removed outlier: 7.692A pdb=" N PHE B 415 " --> pdb=" O THR B 541 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR B 541 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 540 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE B 493 " --> pdb=" O GLN B 566 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N LEU B 568 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 495 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N CYS B 570 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE B 497 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS B 572 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER B 499 " --> pdb=" O LYS B 572 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LYS B 735 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA B 627 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS B 737 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 629 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N SER B 739 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N ILE B 631 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N TYR B 741 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N THR B 633 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER B 743 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 527 through 528 removed outlier: 6.728A pdb=" N GLU B 527 " --> pdb=" O ILE A 982 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 545 through 549 removed outlier: 5.670A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 981 through 982 removed outlier: 6.406A pdb=" N GLU A 527 " --> pdb=" O ILE B 982 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 390 removed outlier: 7.693A pdb=" N PHE A 415 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR A 541 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A 540 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 493 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LEU A 568 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 495 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N CYS A 570 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE A 497 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS A 572 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER A 499 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET A 449 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU A 601 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 451 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LYS A 735 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA A 627 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS A 737 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 629 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N SER A 739 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N ILE A 631 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N TYR A 741 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N THR A 633 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER A 743 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 549 removed outlier: 5.671A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) 661 hydrogen bonds defined for protein. 1890 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: 3.62 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1654 1.31 - 1.43: 3219 1.43 - 1.56: 6189 1.56 - 1.69: 12 1.69 - 1.81: 104 Bond restraints: 11178 Sorted by residual: bond pdb=" C4 UD1 B1503 " pdb=" N3 UD1 B1503 " ideal model delta sigma weight residual 1.386 1.277 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 UD1 A1503 " pdb=" N3 UD1 A1503 " ideal model delta sigma weight residual 1.386 1.278 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C2B UD1 A1503 " pdb=" C3B UD1 A1503 " ideal model delta sigma weight residual 1.533 1.462 0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C2B UD1 B1503 " pdb=" C3B UD1 B1503 " ideal model delta sigma weight residual 1.533 1.462 0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N ILE A 671 " pdb=" CA ILE A 671 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.11e-02 8.12e+03 1.05e+01 ... (remaining 11173 not shown) Histogram of bond angle deviations from ideal: 91.07 - 99.70: 6 99.70 - 108.34: 461 108.34 - 116.97: 7032 116.97 - 125.61: 7518 125.61 - 134.24: 163 Bond angle restraints: 15180 Sorted by residual: angle pdb=" C1B UD1 B1503 " pdb=" C2B UD1 B1503 " pdb=" O2' UD1 B1503 " ideal model delta sigma weight residual 109.46 130.35 -20.89 3.00e+00 1.11e-01 4.85e+01 angle pdb=" C1B UD1 A1503 " pdb=" C2B UD1 A1503 " pdb=" O2' UD1 A1503 " ideal model delta sigma weight residual 109.46 130.35 -20.89 3.00e+00 1.11e-01 4.85e+01 angle pdb=" C MET B 992 " pdb=" CA MET B 992 " pdb=" CB MET B 992 " ideal model delta sigma weight residual 116.54 109.41 7.13 1.15e+00 7.56e-01 3.85e+01 angle pdb=" C MET A 992 " pdb=" CA MET A 992 " pdb=" CB MET A 992 " ideal model delta sigma weight residual 116.63 109.53 7.10 1.16e+00 7.43e-01 3.74e+01 angle pdb=" C2B UD1 B1503 " pdb=" C1B UD1 B1503 " pdb=" O4B UD1 B1503 " ideal model delta sigma weight residual 106.74 91.07 15.67 3.00e+00 1.11e-01 2.73e+01 ... (remaining 15175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 6384 33.90 - 67.80: 188 67.80 - 101.70: 30 101.70 - 135.60: 6 135.60 - 169.51: 2 Dihedral angle restraints: 6610 sinusoidal: 2516 harmonic: 4094 Sorted by residual: dihedral pdb=" C27 POV B1502 " pdb=" C28 POV B1502 " pdb=" C29 POV B1502 " pdb="C210 POV B1502 " ideal model delta sinusoidal sigma weight residual 127.48 -63.01 -169.51 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C27 POV A1502 " pdb=" C28 POV A1502 " pdb=" C29 POV A1502 " pdb="C210 POV A1502 " ideal model delta sinusoidal sigma weight residual 127.48 -63.01 -169.51 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA PRO A 410 " pdb=" C PRO A 410 " pdb=" N ASN A 411 " pdb=" CA ASN A 411 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 6607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1453 0.090 - 0.180: 252 0.180 - 0.271: 20 0.271 - 0.361: 6 0.361 - 0.451: 4 Chirality restraints: 1735 Sorted by residual: chirality pdb=" C2B UD1 A1503 " pdb=" C1B UD1 A1503 " pdb=" C3B UD1 A1503 " pdb=" O2' UD1 A1503 " both_signs ideal model delta sigma weight residual False -2.62 -2.17 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C2B UD1 B1503 " pdb=" C1B UD1 B1503 " pdb=" C3B UD1 B1503 " pdb=" O2' UD1 B1503 " both_signs ideal model delta sigma weight residual False -2.62 -2.17 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C5' UD1 B1503 " pdb=" C4' UD1 B1503 " pdb=" C6' UD1 B1503 " pdb=" O5' UD1 B1503 " both_signs ideal model delta sigma weight residual False -2.52 -2.10 -0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 1732 not shown) Planarity restraints: 1859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2' UD1 B1503 " 0.169 2.00e-02 2.50e+03 1.36e-01 2.32e+02 pdb=" C7' UD1 B1503 " -0.055 2.00e-02 2.50e+03 pdb=" C8' UD1 B1503 " 0.133 2.00e-02 2.50e+03 pdb=" N2' UD1 B1503 " -0.204 2.00e-02 2.50e+03 pdb=" O7' UD1 B1503 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2' UD1 A1503 " 0.169 2.00e-02 2.50e+03 1.36e-01 2.32e+02 pdb=" C7' UD1 A1503 " -0.055 2.00e-02 2.50e+03 pdb=" C8' UD1 A1503 " 0.133 2.00e-02 2.50e+03 pdb=" N2' UD1 A1503 " -0.204 2.00e-02 2.50e+03 pdb=" O7' UD1 A1503 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 696 " -0.016 2.00e-02 2.50e+03 1.62e-02 5.24e+00 pdb=" CG TYR A 696 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 696 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 696 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 696 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 696 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 696 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 696 " 0.004 2.00e-02 2.50e+03 ... (remaining 1856 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2899 2.81 - 3.33: 10904 3.33 - 3.85: 17859 3.85 - 4.38: 20609 4.38 - 4.90: 36151 Nonbonded interactions: 88422 Sorted by model distance: nonbonded pdb=" O3' UD1 A1503 " pdb=" O7' UD1 A1503 " model vdw 2.285 2.440 nonbonded pdb=" O3' UD1 B1503 " pdb=" O7' UD1 B1503 " model vdw 2.285 2.440 nonbonded pdb=" O CYS A 845 " pdb=" OG1 THR A 849 " model vdw 2.351 2.440 nonbonded pdb=" O CYS B 845 " pdb=" OG1 THR B 849 " model vdw 2.352 2.440 nonbonded pdb=" O ILE B 844 " pdb=" OG SER B 848 " model vdw 2.356 2.440 ... (remaining 88417 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' and (resid 381 through 501 or (resid 502 and (name N or name CA or na \ me C or name O or name CB )) or resid 503 or (resid 504 and (name N or name CA o \ r name C or name O or name CB )) or resid 505 through 664 or (resid 665 and (nam \ e N or name CA or name C or name O or name CB )) or resid 666 through 670 or (re \ sid 671 and (name N or name CA or name C or name O or name CB )) or resid 672 th \ rough 716 or (resid 717 and (name N or name CA or name C or name O or name CB )) \ or resid 718 or (resid 719 and (name N or name CA or name C or name O or name C \ B )) or resid 720 through 981 or (resid 982 through 987 and (name N or name CA o \ r name C or name O or name CB )) or (resid 988 through 997 and (name N or name C \ A or name C or name O or name CB )) or resid 998 through 1127 or resid 1501 thro \ ugh 1503)) selection = (chain 'B' and (resid 381 through 449 or (resid 450 through 452 and (name N or n \ ame CA or name C or name O or name CB )) or resid 453 through 673 or (resid 674 \ and (name N or name CA or name C or name O or name CB )) or resid 675 through 11 \ 27 or resid 1501 through 1503)) } 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: 1.450 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: 6.750 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.270 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 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 : 0.009 0.109 11178 Z= 0.574 Angle : 1.123 20.895 15180 Z= 0.704 Chirality : 0.070 0.451 1735 Planarity : 0.006 0.136 1859 Dihedral : 17.131 169.506 3962 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.89 % Allowed : 1.81 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.23), residues: 1364 helix: 1.09 (0.19), residues: 772 sheet: -1.74 (0.44), residues: 120 loop : -1.34 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 779 HIS 0.004 0.001 HIS B 783 PHE 0.020 0.002 PHE B 885 TYR 0.040 0.002 TYR A 696 ARG 0.004 0.001 ARG B 436 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 241 time to evaluate : 1.129 Fit side-chains REVERT: B 579 ILE cc_start: 0.8138 (tt) cc_final: 0.7933 (mm) REVERT: B 700 MET cc_start: 0.2571 (tmm) cc_final: 0.2363 (mmt) REVERT: B 932 TYR cc_start: 0.7042 (t80) cc_final: 0.6832 (t80) REVERT: A 579 ILE cc_start: 0.8100 (tt) cc_final: 0.7876 (mm) REVERT: A 932 TYR cc_start: 0.7027 (t80) cc_final: 0.6817 (t80) REVERT: A 952 TYR cc_start: 0.7335 (m-10) cc_final: 0.7112 (m-10) outliers start: 32 outliers final: 2 residues processed: 265 average time/residue: 0.9517 time to fit residues: 274.1068 Evaluate side-chains 145 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain A residue 394 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.0010 chunk 80 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN B1004 ASN B1013 ASN A 965 HIS A 977 ASN A1002 GLN A1004 ASN A1013 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11178 Z= 0.169 Angle : 0.512 9.980 15180 Z= 0.269 Chirality : 0.040 0.149 1735 Planarity : 0.004 0.043 1859 Dihedral : 10.997 148.924 1683 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.34 % Allowed : 13.18 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.24), residues: 1364 helix: 2.30 (0.19), residues: 760 sheet: -0.99 (0.43), residues: 132 loop : -0.57 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1047 HIS 0.004 0.001 HIS A 459 PHE 0.018 0.002 PHE A1052 TYR 0.017 0.001 TYR A 827 ARG 0.004 0.000 ARG A 718 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 163 time to evaluate : 0.833 Fit side-chains REVERT: B 594 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7621 (mpt-90) REVERT: B 655 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7121 (mmmt) REVERT: B 700 MET cc_start: 0.2850 (tmm) cc_final: 0.2093 (mmm) REVERT: B 886 MET cc_start: 0.6825 (mtm) cc_final: 0.6291 (mmm) REVERT: B 932 TYR cc_start: 0.7278 (t80) cc_final: 0.6837 (t80) REVERT: B 938 MET cc_start: 0.7885 (tpt) cc_final: 0.7615 (mmm) REVERT: B 943 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.7978 (pt) REVERT: B 952 TYR cc_start: 0.7372 (m-10) cc_final: 0.7034 (m-10) REVERT: A 579 ILE cc_start: 0.8126 (tt) cc_final: 0.7899 (mm) REVERT: A 594 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7624 (mpt-90) REVERT: A 655 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7147 (mmmt) REVERT: A 692 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7280 (tp40) REVERT: A 886 MET cc_start: 0.6833 (mtm) cc_final: 0.6306 (mmm) REVERT: A 932 TYR cc_start: 0.7269 (t80) cc_final: 0.6829 (t80) outliers start: 37 outliers final: 11 residues processed: 189 average time/residue: 0.8828 time to fit residues: 183.5488 Evaluate side-chains 142 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1090 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 0.0980 chunk 85 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 0.0020 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 934 GLN B 977 ASN A 398 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11178 Z= 0.255 Angle : 0.565 6.263 15180 Z= 0.305 Chirality : 0.042 0.157 1735 Planarity : 0.004 0.045 1859 Dihedral : 10.627 139.931 1681 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.42 % Allowed : 13.90 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.59 (0.24), residues: 1364 helix: 2.36 (0.19), residues: 758 sheet: -0.56 (0.43), residues: 148 loop : -0.63 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 806 HIS 0.005 0.002 HIS B 459 PHE 0.018 0.002 PHE B1052 TYR 0.014 0.002 TYR A 538 ARG 0.005 0.001 ARG B 718 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 139 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 594 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7813 (mpt-90) REVERT: B 631 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7160 (tp) REVERT: B 655 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7165 (mmmt) REVERT: B 886 MET cc_start: 0.6413 (mtm) cc_final: 0.5870 (mmm) REVERT: B 943 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8248 (pt) REVERT: A 594 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7805 (mpt-90) REVERT: A 655 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7319 (mtpt) REVERT: A 692 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7260 (tp40) REVERT: A 700 MET cc_start: 0.4993 (OUTLIER) cc_final: 0.4367 (mmt) REVERT: A 886 MET cc_start: 0.6430 (mtm) cc_final: 0.5866 (mmm) REVERT: A 932 TYR cc_start: 0.7228 (t80) cc_final: 0.6858 (t80) REVERT: A 982 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6806 (pt) outliers start: 49 outliers final: 26 residues processed: 168 average time/residue: 0.8950 time to fit residues: 166.2295 Evaluate side-chains 163 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 65 optimal weight: 0.0010 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11178 Z= 0.202 Angle : 0.497 7.542 15180 Z= 0.266 Chirality : 0.040 0.160 1735 Planarity : 0.004 0.045 1859 Dihedral : 10.377 132.772 1681 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.24 % Allowed : 14.89 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.24), residues: 1364 helix: 2.57 (0.19), residues: 758 sheet: -0.44 (0.42), residues: 148 loop : -0.59 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 806 HIS 0.004 0.001 HIS B 459 PHE 0.023 0.002 PHE B1124 TYR 0.010 0.001 TYR A 713 ARG 0.003 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 133 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 523 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.5834 (p90) REVERT: B 655 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7243 (mmmt) REVERT: B 886 MET cc_start: 0.6413 (mtm) cc_final: 0.5866 (mmm) REVERT: B 943 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8211 (pt) REVERT: A 523 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.5853 (p90) REVERT: A 655 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7286 (mmmt) REVERT: A 717 ASP cc_start: 0.4932 (t0) cc_final: 0.4643 (t0) REVERT: A 982 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6703 (pt) outliers start: 47 outliers final: 27 residues processed: 163 average time/residue: 0.8091 time to fit residues: 145.6450 Evaluate side-chains 162 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 977 ASN Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 982 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 99 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11178 Z= 0.154 Angle : 0.455 6.869 15180 Z= 0.243 Chirality : 0.039 0.152 1735 Planarity : 0.003 0.043 1859 Dihedral : 10.032 130.487 1681 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.70 % Allowed : 16.34 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.24), residues: 1364 helix: 2.79 (0.19), residues: 758 sheet: -0.30 (0.43), residues: 148 loop : -0.57 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 806 HIS 0.003 0.001 HIS B 459 PHE 0.016 0.001 PHE A1052 TYR 0.017 0.001 TYR B 827 ARG 0.002 0.000 ARG A 718 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 135 time to evaluate : 1.192 Fit side-chains REVERT: B 655 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7236 (mmmt) REVERT: B 832 ASN cc_start: 0.6027 (OUTLIER) cc_final: 0.5755 (m-40) REVERT: B 886 MET cc_start: 0.6464 (mtm) cc_final: 0.5932 (mmm) REVERT: B 943 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8257 (pt) REVERT: A 655 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7268 (mmmt) REVERT: A 700 MET cc_start: 0.4936 (OUTLIER) cc_final: 0.4344 (mmt) REVERT: A 832 ASN cc_start: 0.6030 (OUTLIER) cc_final: 0.5764 (m-40) REVERT: A 886 MET cc_start: 0.6545 (mtm) cc_final: 0.5975 (mmm) REVERT: A 982 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6700 (pt) REVERT: A 1124 PHE cc_start: 0.7994 (t80) cc_final: 0.7768 (t80) outliers start: 41 outliers final: 24 residues processed: 165 average time/residue: 0.7889 time to fit residues: 143.5692 Evaluate side-chains 158 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 977 ASN Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11178 Z= 0.198 Angle : 0.484 6.531 15180 Z= 0.259 Chirality : 0.040 0.154 1735 Planarity : 0.003 0.042 1859 Dihedral : 10.088 133.004 1681 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.69 % Allowed : 16.16 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.89 (0.24), residues: 1364 helix: 2.64 (0.18), residues: 770 sheet: -0.31 (0.42), residues: 150 loop : -0.71 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 806 HIS 0.004 0.001 HIS B 459 PHE 0.017 0.002 PHE A1052 TYR 0.010 0.001 TYR A 797 ARG 0.002 0.000 ARG B 718 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 128 time to evaluate : 1.161 Fit side-chains REVERT: B 523 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.5716 (p90) REVERT: B 655 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7220 (mmmt) REVERT: B 692 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.6790 (mp-120) REVERT: B 832 ASN cc_start: 0.6154 (OUTLIER) cc_final: 0.5883 (m-40) REVERT: B 943 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8268 (pt) REVERT: A 523 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.5717 (p90) REVERT: A 655 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7275 (mmmt) REVERT: A 700 MET cc_start: 0.4924 (OUTLIER) cc_final: 0.4309 (mmt) REVERT: A 832 ASN cc_start: 0.6157 (OUTLIER) cc_final: 0.5890 (m-40) outliers start: 52 outliers final: 31 residues processed: 165 average time/residue: 0.7126 time to fit residues: 129.7551 Evaluate side-chains 162 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 122 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 759 ARG Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 977 ASN Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 0.0060 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 0.0060 chunk 81 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.4812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 545 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11178 Z= 0.148 Angle : 0.448 6.474 15180 Z= 0.240 Chirality : 0.039 0.151 1735 Planarity : 0.003 0.042 1859 Dihedral : 9.833 130.370 1681 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.97 % Allowed : 16.79 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.09 (0.24), residues: 1364 helix: 2.81 (0.18), residues: 770 sheet: -0.15 (0.42), residues: 150 loop : -0.68 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 806 HIS 0.002 0.001 HIS B 459 PHE 0.015 0.001 PHE B 415 TYR 0.017 0.001 TYR A 827 ARG 0.002 0.000 ARG A 718 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 0.900 Fit side-chains REVERT: B 523 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.5466 (p90) REVERT: B 655 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7230 (mmmt) REVERT: B 943 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8294 (pt) REVERT: B 1124 PHE cc_start: 0.7902 (t80) cc_final: 0.7698 (t80) REVERT: A 476 MET cc_start: 0.7490 (mtm) cc_final: 0.7239 (ttm) REVERT: A 523 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.5573 (p90) REVERT: A 655 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7290 (mmmt) REVERT: A 700 MET cc_start: 0.4708 (OUTLIER) cc_final: 0.4171 (mmt) outliers start: 44 outliers final: 28 residues processed: 164 average time/residue: 0.7133 time to fit residues: 129.2344 Evaluate side-chains 168 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 977 ASN Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 759 ARG Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 65 optimal weight: 0.0040 chunk 12 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -build -allalt -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: