Starting phenix.real_space_refine on Thu Mar 5 03:35:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tno_26016/03_2026/7tno_26016.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tno_26016/03_2026/7tno_26016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tno_26016/03_2026/7tno_26016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tno_26016/03_2026/7tno_26016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tno_26016/03_2026/7tno_26016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tno_26016/03_2026/7tno_26016.map" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 S 136 5.16 5 Cl 4 4.86 5 C 12198 2.51 5 N 3044 2.21 5 O 3428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18810 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4673 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4667 Classifications: {'peptide': 600} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 584} Chain breaks: 4 Chain: "C" Number of atoms: 4673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4673 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4671 Classifications: {'peptide': 600} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 584} Chain breaks: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.10, per 1000 atoms: 0.22 Number of scatterers: 18810 At special positions: 0 Unit cell: (125.33, 115.37, 136.95, 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) Cl 4 17.00 S 136 16.00 O 3428 8.00 N 3044 7.00 C 12198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.04 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.04 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.02 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 825.0 milliseconds 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4390 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 24 sheets defined 55.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 removed outlier: 4.327A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.542A pdb=" N TYR A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.613A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.740A pdb=" N THR A 568 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 569' Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 595 through 626 removed outlier: 3.570A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 642 Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.645A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.744A pdb=" N TYR A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.535A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.514A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.672A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.616A pdb=" N LYS A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 822 removed outlier: 4.358A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG A 819 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1029 removed outlier: 3.812A pdb=" N LEU A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1103 removed outlier: 3.597A pdb=" N LEU A1097 " --> pdb=" O ALA A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1123 Processing helix chain 'A' and resid 1132 through 1160 removed outlier: 3.617A pdb=" N VAL A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A1155 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1160 " --> pdb=" O ILE A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1207 removed outlier: 3.597A pdb=" N GLY A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A1187 " --> pdb=" O ALA A1183 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A1197 " --> pdb=" O GLY A1193 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.595A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.695A pdb=" N VAL B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.651A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.516A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 545 removed outlier: 3.574A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 597 through 617 removed outlier: 4.157A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.504A pdb=" N PHE B 623 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 619 through 624' Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.827A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 4.375A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 removed outlier: 3.505A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 743 through 756 removed outlier: 4.251A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 770 removed outlier: 3.502A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 770 " --> pdb=" O TRP B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 777 removed outlier: 3.508A pdb=" N LYS B 776 " --> pdb=" O CYS B 773 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP B 777 " --> pdb=" O GLY B 774 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 773 through 777' Processing helix chain 'B' and resid 793 through 819 removed outlier: 3.543A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 819 " --> pdb=" O CYS B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1028 removed outlier: 3.858A pdb=" N GLN B1008 " --> pdb=" O ASP B1004 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B1009 " --> pdb=" O ARG B1005 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1104 Processing helix chain 'B' and resid 1104 through 1123 removed outlier: 3.525A pdb=" N CYS B1120 " --> pdb=" O MET B1116 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1160 removed outlier: 3.593A pdb=" N VAL B1154 " --> pdb=" O ILE B1150 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B1158 " --> pdb=" O VAL B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1209 removed outlier: 3.709A pdb=" N TYR B1180 " --> pdb=" O GLY B1176 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B1187 " --> pdb=" O ALA B1183 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B1197 " --> pdb=" O GLY B1193 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 462 through 469 removed outlier: 3.571A pdb=" N GLU C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.520A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.589A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.805A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 569 removed outlier: 3.673A pdb=" N ASN C 569 " --> pdb=" O GLU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 623 removed outlier: 3.876A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 621 " --> pdb=" O THR C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 641 removed outlier: 3.516A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.749A pdb=" N TYR C 673 " --> pdb=" O LYS C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 697 Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.592A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 756 Processing helix chain 'C' and resid 757 through 767 Processing helix chain 'C' and resid 792 through 822 removed outlier: 4.082A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1029 removed outlier: 3.622A pdb=" N THR C1012 " --> pdb=" O GLN C1008 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE C1017 " --> pdb=" O THR C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1104 Processing helix chain 'C' and resid 1104 through 1126 removed outlier: 3.904A pdb=" N LEU C1114 " --> pdb=" O SER C1110 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU C1125 " --> pdb=" O ILE C1121 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE C1126 " --> pdb=" O ALA C1122 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1160 removed outlier: 3.678A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C1145 " --> pdb=" O PHE C1141 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C1150 " --> pdb=" O LEU C1146 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C1158 " --> pdb=" O VAL C1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1208 removed outlier: 3.549A pdb=" N ILE C1187 " --> pdb=" O ALA C1183 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C1189 " --> pdb=" O SER C1185 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C1197 " --> pdb=" O GLY C1193 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.761A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.594A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 458 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.507A pdb=" N GLU D 486 " --> pdb=" O THR D 482 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 482 through 487' Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 545 removed outlier: 3.642A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 616 removed outlier: 3.736A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 625 removed outlier: 3.670A pdb=" N PHE D 623 " --> pdb=" O ASN D 619 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 4.124A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.581A pdb=" N PHE D 658 " --> pdb=" O SER D 654 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.871A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.614A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.578A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 removed outlier: 3.711A pdb=" N ASN D 764 " --> pdb=" O ASP D 760 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 765 " --> pdb=" O LYS D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 819 Processing helix chain 'D' and resid 1007 through 1029 Processing helix chain 'D' and resid 1092 through 1103 removed outlier: 3.994A pdb=" N VAL D1100 " --> pdb=" O PHE D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1123 removed outlier: 3.592A pdb=" N LEU D1114 " --> pdb=" O SER D1110 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS D1120 " --> pdb=" O MET D1116 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA D1122 " --> pdb=" O GLY D1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1161 removed outlier: 3.554A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D1142 " --> pdb=" O GLY D1138 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D1150 " --> pdb=" O LEU D1146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY D1161 " --> pdb=" O SER D1157 " (cutoff:3.500A) Processing helix chain 'D' and resid 1176 through 1208 removed outlier: 3.531A pdb=" N ILE D1187 " --> pdb=" O ALA D1183 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D1197 " --> pdb=" O GLY D1193 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS D1204 " --> pdb=" O PHE D1200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.974A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.265A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.582A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1064 through 1067 removed outlier: 3.874A pdb=" N LEU A1075 " --> pdb=" O CYS A1067 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.801A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB1, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 5.893A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 5.893A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1076 through 1078 Processing sheet with id=AB5, first strand: chain 'C' and resid 397 through 399 removed outlier: 6.084A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'C' and resid 489 through 498 removed outlier: 5.241A pdb=" N ILE C 734 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR C 732 " --> pdb=" O PRO C 494 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET C 496 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS C 730 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.269A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1064 through 1065 Processing sheet with id=AC1, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AC2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC4, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.686A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 646 through 648 removed outlier: 3.637A pdb=" N LEU D 703 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1077 through 1078 removed outlier: 3.871A pdb=" N CYS D1066 " --> pdb=" O HIS D1059 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D1035 " --> pdb=" O THR D1058 " (cutoff:3.500A) 962 hydrogen bonds defined for protein. 2811 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: 2.83 Time building geometry restraints manager: 1.97 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: 5732 1.34 - 1.47: 4929 1.47 - 1.59: 8338 1.59 - 1.71: 8 1.71 - 1.83: 220 Bond restraints: 19227 Sorted by residual: bond pdb=" N LYS C 449 " pdb=" CA LYS C 449 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 9.03e+00 bond pdb=" N ILE C 459 " pdb=" CA ILE C 459 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.72e+00 bond pdb=" N ARG C 453 " pdb=" CA ARG C 453 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.49e+00 bond pdb=" N ASP C 454 " pdb=" CA ASP C 454 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.78e+00 bond pdb=" N LYS A 449 " pdb=" CA LYS A 449 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.33e-02 5.65e+03 6.78e+00 ... (remaining 19222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 25331 2.48 - 4.96: 524 4.96 - 7.44: 95 7.44 - 9.92: 20 9.92 - 12.40: 5 Bond angle restraints: 25975 Sorted by residual: angle pdb=" C PRO D 507 " pdb=" N GLN D 508 " pdb=" CA GLN D 508 " ideal model delta sigma weight residual 121.54 133.70 -12.16 1.91e+00 2.74e-01 4.05e+01 angle pdb=" C GLN D 508 " pdb=" N LYS D 509 " pdb=" CA LYS D 509 " ideal model delta sigma weight residual 121.54 132.92 -11.38 1.91e+00 2.74e-01 3.55e+01 angle pdb=" C ALA D1086 " pdb=" N ASP D1087 " pdb=" CA ASP D1087 " ideal model delta sigma weight residual 121.54 131.82 -10.28 1.91e+00 2.74e-01 2.90e+01 angle pdb=" C ARG D1130 " pdb=" N HIS D1131 " pdb=" CA HIS D1131 " ideal model delta sigma weight residual 122.08 129.44 -7.36 1.47e+00 4.63e-01 2.51e+01 angle pdb=" N ASN B1132 " pdb=" CA ASN B1132 " pdb=" C ASN B1132 " ideal model delta sigma weight residual 114.75 108.86 5.89 1.26e+00 6.30e-01 2.19e+01 ... (remaining 25970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 10969 24.44 - 48.87: 354 48.87 - 73.31: 24 73.31 - 97.74: 12 97.74 - 122.18: 9 Dihedral angle restraints: 11368 sinusoidal: 4488 harmonic: 6880 Sorted by residual: dihedral pdb=" CA GLN D 508 " pdb=" C GLN D 508 " pdb=" N LYS D 509 " pdb=" CA LYS D 509 " ideal model delta harmonic sigma weight residual 180.00 138.33 41.67 0 5.00e+00 4.00e-02 6.95e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 166.76 -73.76 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 166.46 -73.46 1 1.00e+01 1.00e-02 6.87e+01 ... (remaining 11365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2321 0.059 - 0.118: 483 0.118 - 0.178: 95 0.178 - 0.237: 7 0.237 - 0.296: 5 Chirality restraints: 2911 Sorted by residual: chirality pdb=" C1 CYZ A1302 " pdb=" C2 CYZ A1302 " pdb=" C6 CYZ A1302 " pdb=" C8 CYZ A1302 " both_signs ideal model delta sigma weight residual False 2.79 2.50 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C1 CYZ D1301 " pdb=" C2 CYZ D1301 " pdb=" C6 CYZ D1301 " pdb=" C8 CYZ D1301 " both_signs ideal model delta sigma weight residual False 2.79 2.51 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C8 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" N2 CYZ C1302 " both_signs ideal model delta sigma weight residual False 2.20 2.48 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2908 not shown) Planarity restraints: 3188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 447 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C ASP C 447 " -0.057 2.00e-02 2.50e+03 pdb=" O ASP C 447 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY C 448 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 566 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C GLU D 566 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU D 566 " -0.015 2.00e-02 2.50e+03 pdb=" N SER D 567 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO C 717 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.028 5.00e-02 4.00e+02 ... (remaining 3185 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 113 2.60 - 3.17: 15425 3.17 - 3.75: 28580 3.75 - 4.32: 39920 4.32 - 4.90: 64209 Nonbonded interactions: 148247 Sorted by model distance: nonbonded pdb=" OD1 ASP B 760 " pdb="CL CYZ B1302 " model vdw 2.023 3.270 nonbonded pdb=" O PHE B 517 " pdb=" OH TYR B 616 " model vdw 2.302 3.040 nonbonded pdb=" OG SER A 597 " pdb=" O ALA B 806 " model vdw 2.310 3.040 nonbonded pdb=" O SER B 564 " pdb=" OG1 THR B 568 " model vdw 2.313 3.040 nonbonded pdb=" O PHE D 517 " pdb=" OH TYR D 616 " model vdw 2.315 3.040 ... (remaining 148242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 819 or resid 1002 through 1169 or resid 1171 t \ hrough 1208 or resid 1302)) selection = (chain 'B' and (resid 394 through 548 or (resid 563 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 819 or resid 1002 through 1041 \ or resid 1056 through 1208 or resid 1302)) selection = (chain 'C' and (resid 394 through 819 or resid 1002 through 1169 or resid 1171 t \ hrough 1208 or resid 1302)) selection = (chain 'D' and (resid 394 through 548 or (resid 563 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 1041 or resid 1056 through 116 \ 9 or resid 1171 through 1208 or resid 1301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.360 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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 : 0.004 0.060 19239 Z= 0.229 Angle : 0.939 12.405 25999 Z= 0.525 Chirality : 0.051 0.296 2911 Planarity : 0.006 0.058 3188 Dihedral : 12.110 122.178 6942 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 0.65 % Allowed : 5.24 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.12 (0.11), residues: 2362 helix: -3.93 (0.06), residues: 1303 sheet: -2.15 (0.39), residues: 156 loop : -2.42 (0.16), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 692 TYR 0.028 0.002 TYR B1031 PHE 0.028 0.002 PHE B1072 TRP 0.029 0.003 TRP A1032 HIS 0.006 0.002 HIS B1081 Details of bonding type rmsd covalent geometry : bond 0.00445 (19227) covalent geometry : angle 0.93867 (25975) SS BOND : bond 0.00556 ( 12) SS BOND : angle 1.38411 ( 24) hydrogen bonds : bond 0.29804 ( 958) hydrogen bonds : angle 9.37486 ( 2811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 711 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7272 (mtmt) REVERT: A 511 LYS cc_start: 0.6826 (mttp) cc_final: 0.6082 (tptt) REVERT: A 600 ILE cc_start: 0.9377 (mt) cc_final: 0.9123 (mm) REVERT: A 654 SER cc_start: 0.8564 (p) cc_final: 0.8195 (m) REVERT: A 680 SER cc_start: 0.6957 (p) cc_final: 0.6362 (t) REVERT: A 723 VAL cc_start: 0.8267 (m) cc_final: 0.8025 (t) REVERT: A 1030 ASP cc_start: 0.5668 (p0) cc_final: 0.4400 (p0) REVERT: A 1063 TRP cc_start: 0.7834 (m100) cc_final: 0.7435 (m-10) REVERT: A 1130 ARG cc_start: 0.7809 (mmp-170) cc_final: 0.7472 (mmm160) REVERT: A 1147 SER cc_start: 0.8542 (t) cc_final: 0.8318 (p) REVERT: A 1148 ASN cc_start: 0.8342 (t0) cc_final: 0.7951 (t0) REVERT: B 498 LEU cc_start: 0.8853 (pt) cc_final: 0.8584 (pp) REVERT: B 519 ASP cc_start: 0.8442 (m-30) cc_final: 0.7887 (t70) REVERT: B 524 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7140 (pt0) REVERT: B 537 SER cc_start: 0.8966 (m) cc_final: 0.8597 (m) REVERT: B 585 MET cc_start: 0.8381 (mmt) cc_final: 0.8167 (mmm) REVERT: B 620 LEU cc_start: 0.8065 (tp) cc_final: 0.7752 (tp) REVERT: B 661 ARG cc_start: 0.5955 (mmp80) cc_final: 0.5687 (ptp90) REVERT: B 1021 SER cc_start: 0.8410 (m) cc_final: 0.8101 (p) REVERT: B 1022 LEU cc_start: 0.8408 (mt) cc_final: 0.8192 (mp) REVERT: B 1148 ASN cc_start: 0.8770 (t0) cc_final: 0.8553 (t0) REVERT: B 1187 ILE cc_start: 0.9218 (mt) cc_final: 0.8990 (mt) REVERT: C 438 PHE cc_start: 0.5883 (p90) cc_final: 0.5581 (p90) REVERT: C 460 TRP cc_start: 0.5889 (m100) cc_final: 0.5573 (m100) REVERT: C 498 LEU cc_start: 0.8354 (pp) cc_final: 0.7740 (pp) REVERT: C 501 SER cc_start: 0.8390 (p) cc_final: 0.8080 (t) REVERT: C 683 VAL cc_start: 0.7310 (m) cc_final: 0.6258 (m) REVERT: C 699 LYS cc_start: 0.8011 (mptt) cc_final: 0.7672 (mmmt) REVERT: C 711 TYR cc_start: 0.7413 (t80) cc_final: 0.7208 (t80) REVERT: C 732 TYR cc_start: 0.7976 (m-10) cc_final: 0.7644 (m-10) REVERT: C 764 ASN cc_start: 0.7857 (m-40) cc_final: 0.7571 (t0) REVERT: C 817 LYS cc_start: 0.7905 (mmpt) cc_final: 0.7646 (mmmt) REVERT: C 1031 TYR cc_start: 0.3906 (p90) cc_final: 0.3599 (p90) REVERT: C 1036 ARG cc_start: 0.6959 (mmt180) cc_final: 0.6702 (mmt-90) REVERT: C 1096 PHE cc_start: 0.7792 (t80) cc_final: 0.7494 (t80) REVERT: C 1120 CYS cc_start: 0.7700 (m) cc_final: 0.7255 (m) REVERT: C 1126 PHE cc_start: 0.6413 (m-10) cc_final: 0.5863 (m-80) REVERT: C 1169 LYS cc_start: 0.2793 (tptp) cc_final: 0.1149 (ptmt) REVERT: D 425 CYS cc_start: 0.7947 (m) cc_final: 0.7683 (m) REVERT: D 476 ILE cc_start: 0.8670 (mt) cc_final: 0.8432 (mp) REVERT: D 533 TYR cc_start: 0.8753 (t80) cc_final: 0.8484 (t80) REVERT: D 637 GLU cc_start: 0.8196 (pp20) cc_final: 0.7684 (pp20) REVERT: D 639 LEU cc_start: 0.7958 (tp) cc_final: 0.7574 (tp) REVERT: D 720 THR cc_start: 0.8010 (p) cc_final: 0.7641 (p) REVERT: D 764 ASN cc_start: 0.7839 (p0) cc_final: 0.7548 (p0) REVERT: D 770 LYS cc_start: 0.7155 (mmmt) cc_final: 0.6657 (mmtt) REVERT: D 1170 LYS cc_start: 0.5128 (tptp) cc_final: 0.4851 (ptpp) REVERT: D 1173 TYR cc_start: 0.6761 (p90) cc_final: 0.6479 (p90) outliers start: 13 outliers final: 2 residues processed: 721 average time/residue: 0.1339 time to fit residues: 145.4931 Evaluate side-chains 422 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 419 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 619 ASN A1204 HIS B 411 ASN B 587 GLN B 791 ASN B1131 HIS B1204 HIS C1059 HIS ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN D 791 ASN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN D1204 HIS D1206 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.130671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105004 restraints weight = 38796.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107413 restraints weight = 23975.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108999 restraints weight = 17797.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109803 restraints weight = 14762.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110499 restraints weight = 13276.371| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19239 Z= 0.140 Angle : 0.622 11.022 25999 Z= 0.328 Chirality : 0.041 0.202 2911 Planarity : 0.005 0.063 3188 Dihedral : 8.886 106.075 2697 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 0.20 % Allowed : 3.74 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.15), residues: 2362 helix: -0.90 (0.12), residues: 1308 sheet: -1.85 (0.37), residues: 181 loop : -2.06 (0.18), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1005 TYR 0.020 0.001 TYR C1031 PHE 0.019 0.002 PHE B1072 TRP 0.020 0.002 TRP C 766 HIS 0.004 0.001 HIS B1081 Details of bonding type rmsd covalent geometry : bond 0.00309 (19227) covalent geometry : angle 0.61823 (25975) SS BOND : bond 0.01393 ( 12) SS BOND : angle 2.25281 ( 24) hydrogen bonds : bond 0.04374 ( 958) hydrogen bonds : angle 4.33924 ( 2811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 515 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7939 (mt) cc_final: 0.7401 (pt) REVERT: A 511 LYS cc_start: 0.6865 (mttp) cc_final: 0.6180 (tptt) REVERT: A 600 ILE cc_start: 0.9273 (mt) cc_final: 0.8964 (mm) REVERT: A 732 TYR cc_start: 0.7835 (m-10) cc_final: 0.7067 (m-80) REVERT: A 1063 TRP cc_start: 0.7816 (m100) cc_final: 0.7428 (m-10) REVERT: A 1130 ARG cc_start: 0.8070 (mmp-170) cc_final: 0.7684 (mmm160) REVERT: A 1199 MET cc_start: 0.7802 (mmm) cc_final: 0.7433 (mmt) REVERT: B 500 ILE cc_start: 0.8893 (mt) cc_final: 0.8590 (mm) REVERT: B 637 GLU cc_start: 0.6516 (mp0) cc_final: 0.6265 (mp0) REVERT: B 776 LYS cc_start: 0.4174 (tttt) cc_final: 0.3960 (tttm) REVERT: B 1008 GLN cc_start: 0.6995 (pt0) cc_final: 0.6683 (pt0) REVERT: B 1021 SER cc_start: 0.8446 (m) cc_final: 0.8155 (p) REVERT: B 1023 MET cc_start: 0.8442 (tpp) cc_final: 0.7756 (tpt) REVERT: B 1065 THR cc_start: 0.6957 (t) cc_final: 0.6125 (m) REVERT: C 400 ILE cc_start: 0.8894 (tp) cc_final: 0.8640 (tp) REVERT: C 432 ILE cc_start: 0.7971 (mm) cc_final: 0.7560 (tp) REVERT: C 438 PHE cc_start: 0.6125 (p90) cc_final: 0.5494 (p90) REVERT: C 817 LYS cc_start: 0.7941 (mmpt) cc_final: 0.7655 (mmmt) REVERT: C 1020 PHE cc_start: 0.8115 (t80) cc_final: 0.7821 (t80) REVERT: C 1031 TYR cc_start: 0.4484 (p90) cc_final: 0.3535 (p90) REVERT: C 1092 THR cc_start: 0.6726 (p) cc_final: 0.6458 (t) REVERT: C 1096 PHE cc_start: 0.7901 (t80) cc_final: 0.7695 (t80) REVERT: C 1130 ARG cc_start: 0.7156 (tpm170) cc_final: 0.6134 (tpt-90) REVERT: C 1169 LYS cc_start: 0.2979 (tptp) cc_final: 0.1458 (ptmt) REVERT: D 420 ARG cc_start: 0.6809 (mtm110) cc_final: 0.6574 (mtm110) REVERT: D 425 CYS cc_start: 0.7829 (m) cc_final: 0.7528 (m) REVERT: D 594 ARG cc_start: 0.8370 (ttp80) cc_final: 0.7870 (ttp80) REVERT: D 639 LEU cc_start: 0.7874 (tp) cc_final: 0.7625 (tt) REVERT: D 712 ILE cc_start: 0.8369 (mm) cc_final: 0.8147 (mt) REVERT: D 1136 SER cc_start: 0.8983 (p) cc_final: 0.8707 (p) REVERT: D 1139 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.7975 (tt) outliers start: 4 outliers final: 0 residues processed: 517 average time/residue: 0.1206 time to fit residues: 96.5541 Evaluate side-chains 374 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 8 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 chunk 194 optimal weight: 0.6980 chunk 237 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS C1059 HIS D 412 HIS D 726 ASN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102725 restraints weight = 39620.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105023 restraints weight = 23918.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.105387 restraints weight = 16358.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105745 restraints weight = 15573.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105838 restraints weight = 14393.174| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19239 Z= 0.177 Angle : 0.645 10.185 25999 Z= 0.336 Chirality : 0.043 0.249 2911 Planarity : 0.004 0.045 3188 Dihedral : 8.371 101.250 2697 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 0.20 % Allowed : 4.64 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.16), residues: 2362 helix: 0.35 (0.14), residues: 1317 sheet: -1.78 (0.38), residues: 183 loop : -1.91 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 453 TYR 0.027 0.002 TYR A 647 PHE 0.023 0.002 PHE C1200 TRP 0.016 0.002 TRP C 460 HIS 0.008 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00411 (19227) covalent geometry : angle 0.64029 (25975) SS BOND : bond 0.00837 ( 12) SS BOND : angle 2.75132 ( 24) hydrogen bonds : bond 0.04118 ( 958) hydrogen bonds : angle 4.16396 ( 2811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 454 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7895 (mt) cc_final: 0.7504 (pt) REVERT: A 425 CYS cc_start: 0.8390 (p) cc_final: 0.8080 (p) REVERT: A 511 LYS cc_start: 0.7061 (mttp) cc_final: 0.6378 (tptt) REVERT: A 600 ILE cc_start: 0.9308 (mt) cc_final: 0.8999 (mm) REVERT: A 721 MET cc_start: 0.7610 (ttp) cc_final: 0.7218 (ttt) REVERT: A 732 TYR cc_start: 0.8002 (m-10) cc_final: 0.7423 (m-80) REVERT: A 1063 TRP cc_start: 0.7878 (m100) cc_final: 0.7412 (m-10) REVERT: A 1130 ARG cc_start: 0.8024 (mmp-170) cc_final: 0.7613 (mmm160) REVERT: A 1199 MET cc_start: 0.7711 (mmm) cc_final: 0.7485 (mmm) REVERT: B 500 ILE cc_start: 0.8995 (mt) cc_final: 0.8648 (mm) REVERT: B 519 ASP cc_start: 0.8517 (m-30) cc_final: 0.8235 (t70) REVERT: B 635 SER cc_start: 0.7530 (p) cc_final: 0.7297 (t) REVERT: B 1008 GLN cc_start: 0.7284 (pt0) cc_final: 0.6837 (pt0) REVERT: B 1021 SER cc_start: 0.8400 (m) cc_final: 0.8065 (p) REVERT: C 400 ILE cc_start: 0.8782 (tp) cc_final: 0.8520 (tp) REVERT: C 438 PHE cc_start: 0.6179 (p90) cc_final: 0.5499 (p90) REVERT: C 501 SER cc_start: 0.8016 (p) cc_final: 0.7729 (t) REVERT: C 817 LYS cc_start: 0.8051 (mmpt) cc_final: 0.7704 (mmmt) REVERT: C 1020 PHE cc_start: 0.8118 (t80) cc_final: 0.7879 (t80) REVERT: C 1031 TYR cc_start: 0.4148 (p90) cc_final: 0.3129 (p90) REVERT: C 1072 PHE cc_start: 0.5925 (m-10) cc_final: 0.5653 (m-80) REVERT: C 1075 LEU cc_start: 0.6182 (mm) cc_final: 0.5514 (tp) REVERT: C 1130 ARG cc_start: 0.7360 (tpm170) cc_final: 0.6070 (tpt-90) REVERT: D 425 CYS cc_start: 0.7993 (m) cc_final: 0.7728 (m) REVERT: D 469 TYR cc_start: 0.6634 (m-80) cc_final: 0.5297 (m-10) REVERT: D 580 SER cc_start: 0.9390 (m) cc_final: 0.8812 (p) REVERT: D 713 GLU cc_start: 0.7133 (tt0) cc_final: 0.6892 (tp30) REVERT: D 1139 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8135 (tt) outliers start: 4 outliers final: 0 residues processed: 456 average time/residue: 0.1168 time to fit residues: 83.6759 Evaluate side-chains 347 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 22 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 182 optimal weight: 0.4980 chunk 178 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1059 HIS D 412 HIS D 435 HIS ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN D1204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105184 restraints weight = 39365.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106397 restraints weight = 23671.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106654 restraints weight = 17444.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106821 restraints weight = 16771.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107869 restraints weight = 15708.309| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19239 Z= 0.123 Angle : 0.586 10.042 25999 Z= 0.303 Chirality : 0.041 0.276 2911 Planarity : 0.004 0.068 3188 Dihedral : 7.719 94.455 2697 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2362 helix: 1.05 (0.14), residues: 1318 sheet: -1.55 (0.42), residues: 157 loop : -1.82 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 594 TYR 0.018 0.001 TYR C 732 PHE 0.021 0.001 PHE A1200 TRP 0.021 0.001 TRP B 460 HIS 0.007 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00276 (19227) covalent geometry : angle 0.57868 (25975) SS BOND : bond 0.01254 ( 12) SS BOND : angle 3.16064 ( 24) hydrogen bonds : bond 0.03490 ( 958) hydrogen bonds : angle 3.81434 ( 2811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 477 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7869 (mt) cc_final: 0.7365 (pt) REVERT: A 476 ILE cc_start: 0.9052 (mt) cc_final: 0.8680 (pt) REVERT: A 511 LYS cc_start: 0.7022 (mttp) cc_final: 0.6314 (tptt) REVERT: A 721 MET cc_start: 0.7431 (ttp) cc_final: 0.7136 (ttt) REVERT: A 732 TYR cc_start: 0.7967 (m-10) cc_final: 0.6274 (m-80) REVERT: A 1063 TRP cc_start: 0.7677 (m100) cc_final: 0.7317 (m-10) REVERT: A 1199 MET cc_start: 0.7698 (mmm) cc_final: 0.7490 (mmt) REVERT: B 500 ILE cc_start: 0.9039 (mt) cc_final: 0.8738 (mm) REVERT: B 519 ASP cc_start: 0.8452 (m-30) cc_final: 0.8179 (t70) REVERT: B 637 GLU cc_start: 0.6562 (mp0) cc_final: 0.6301 (mp0) REVERT: B 1008 GLN cc_start: 0.7227 (pt0) cc_final: 0.6573 (pt0) REVERT: B 1021 SER cc_start: 0.8421 (m) cc_final: 0.8058 (p) REVERT: B 1156 ILE cc_start: 0.8385 (mt) cc_final: 0.8117 (mt) REVERT: C 438 PHE cc_start: 0.5981 (p90) cc_final: 0.5305 (p90) REVERT: C 501 SER cc_start: 0.7953 (p) cc_final: 0.7641 (t) REVERT: C 644 GLU cc_start: 0.6901 (tp30) cc_final: 0.6700 (tp30) REVERT: C 682 PHE cc_start: 0.5221 (m-80) cc_final: 0.5012 (m-80) REVERT: C 817 LYS cc_start: 0.8034 (mmpt) cc_final: 0.7688 (mmmt) REVERT: C 1020 PHE cc_start: 0.8090 (t80) cc_final: 0.7877 (t80) REVERT: C 1031 TYR cc_start: 0.4055 (p90) cc_final: 0.3269 (p90) REVERT: C 1075 LEU cc_start: 0.6457 (mm) cc_final: 0.5572 (tp) REVERT: C 1130 ARG cc_start: 0.7255 (tpm170) cc_final: 0.5864 (tpt-90) REVERT: D 425 CYS cc_start: 0.7929 (m) cc_final: 0.7613 (m) REVERT: D 476 ILE cc_start: 0.8821 (mt) cc_final: 0.8618 (mt) REVERT: D 518 LEU cc_start: 0.8779 (mt) cc_final: 0.8539 (mt) REVERT: D 580 SER cc_start: 0.9324 (m) cc_final: 0.8698 (p) REVERT: D 594 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8217 (ttp80) REVERT: D 644 GLU cc_start: 0.7111 (mp0) cc_final: 0.6518 (tm-30) REVERT: D 752 LYS cc_start: 0.8280 (mtpp) cc_final: 0.7775 (ttmm) REVERT: D 1139 ILE cc_start: 0.8273 (mp) cc_final: 0.8026 (tt) outliers start: 2 outliers final: 0 residues processed: 478 average time/residue: 0.1163 time to fit residues: 87.6796 Evaluate side-chains 372 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.0570 chunk 5 optimal weight: 9.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS C1059 HIS D 586 GLN D 587 GLN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN D1204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.129366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103859 restraints weight = 39162.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106233 restraints weight = 24073.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107871 restraints weight = 17733.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108940 restraints weight = 14635.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109424 restraints weight = 12942.193| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19239 Z= 0.129 Angle : 0.598 10.757 25999 Z= 0.307 Chirality : 0.041 0.270 2911 Planarity : 0.004 0.051 3188 Dihedral : 7.205 90.983 2697 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.10 % Allowed : 2.69 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2362 helix: 1.47 (0.14), residues: 1304 sheet: -1.43 (0.44), residues: 138 loop : -1.75 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 594 TYR 0.018 0.001 TYR A 533 PHE 0.022 0.001 PHE C1200 TRP 0.034 0.002 TRP C 460 HIS 0.011 0.001 HIS D1059 Details of bonding type rmsd covalent geometry : bond 0.00297 (19227) covalent geometry : angle 0.58847 (25975) SS BOND : bond 0.01315 ( 12) SS BOND : angle 3.47032 ( 24) hydrogen bonds : bond 0.03456 ( 958) hydrogen bonds : angle 3.75985 ( 2811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 463 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7805 (mt) cc_final: 0.7298 (pt) REVERT: A 476 ILE cc_start: 0.8988 (mt) cc_final: 0.8628 (pt) REVERT: A 511 LYS cc_start: 0.7012 (mttp) cc_final: 0.6362 (tptt) REVERT: A 600 ILE cc_start: 0.9221 (mt) cc_final: 0.8876 (mm) REVERT: A 732 TYR cc_start: 0.8066 (m-10) cc_final: 0.7430 (m-80) REVERT: A 1008 GLN cc_start: 0.7607 (pt0) cc_final: 0.7403 (mt0) REVERT: A 1063 TRP cc_start: 0.7708 (m100) cc_final: 0.7347 (m-10) REVERT: A 1130 ARG cc_start: 0.7911 (mmt-90) cc_final: 0.7506 (mmm160) REVERT: B 500 ILE cc_start: 0.9065 (mt) cc_final: 0.8772 (mm) REVERT: B 519 ASP cc_start: 0.8549 (m-30) cc_final: 0.8220 (t70) REVERT: B 585 MET cc_start: 0.8544 (mmm) cc_final: 0.8229 (mmm) REVERT: B 1008 GLN cc_start: 0.7223 (pt0) cc_final: 0.6640 (pt0) REVERT: B 1023 MET cc_start: 0.8725 (tpt) cc_final: 0.8506 (tpt) REVERT: B 1115 PHE cc_start: 0.7059 (t80) cc_final: 0.6278 (t80) REVERT: C 438 PHE cc_start: 0.5858 (p90) cc_final: 0.5139 (p90) REVERT: C 473 ASP cc_start: 0.6951 (m-30) cc_final: 0.5127 (t70) REVERT: C 501 SER cc_start: 0.8081 (p) cc_final: 0.7835 (t) REVERT: C 817 LYS cc_start: 0.7990 (mmpt) cc_final: 0.7673 (mmmt) REVERT: C 1031 TYR cc_start: 0.3663 (p90) cc_final: 0.2891 (p90) REVERT: C 1130 ARG cc_start: 0.7120 (tpm170) cc_final: 0.5648 (tpt90) REVERT: C 1156 ILE cc_start: 0.8668 (mt) cc_final: 0.8402 (mp) REVERT: D 405 TYR cc_start: 0.7393 (m-80) cc_final: 0.7169 (m-80) REVERT: D 425 CYS cc_start: 0.7910 (m) cc_final: 0.7616 (m) REVERT: D 469 TYR cc_start: 0.6759 (m-10) cc_final: 0.6442 (m-80) REVERT: D 476 ILE cc_start: 0.8824 (mt) cc_final: 0.8584 (mt) REVERT: D 518 LEU cc_start: 0.8769 (mt) cc_final: 0.8366 (mt) REVERT: D 580 SER cc_start: 0.9277 (m) cc_final: 0.8690 (p) REVERT: D 594 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8234 (ttp80) REVERT: D 644 GLU cc_start: 0.7064 (mp0) cc_final: 0.6588 (tm-30) REVERT: D 766 TRP cc_start: 0.7485 (m100) cc_final: 0.7278 (m100) REVERT: D 816 TYR cc_start: 0.6123 (t80) cc_final: 0.5901 (t80) outliers start: 2 outliers final: 0 residues processed: 464 average time/residue: 0.1197 time to fit residues: 87.7117 Evaluate side-chains 355 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1204 HIS ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN D1204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.127165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.102723 restraints weight = 39670.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104020 restraints weight = 24297.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104598 restraints weight = 17883.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105148 restraints weight = 17335.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105176 restraints weight = 15435.658| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19239 Z= 0.161 Angle : 0.632 13.350 25999 Z= 0.327 Chirality : 0.043 0.272 2911 Planarity : 0.004 0.043 3188 Dihedral : 6.955 90.830 2697 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2362 helix: 1.45 (0.14), residues: 1313 sheet: -1.53 (0.45), residues: 139 loop : -1.82 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 692 TYR 0.020 0.002 TYR C1031 PHE 0.025 0.002 PHE C1200 TRP 0.029 0.002 TRP D 767 HIS 0.006 0.001 HIS D1059 Details of bonding type rmsd covalent geometry : bond 0.00377 (19227) covalent geometry : angle 0.62459 (25975) SS BOND : bond 0.01060 ( 12) SS BOND : angle 3.31626 ( 24) hydrogen bonds : bond 0.03645 ( 958) hydrogen bonds : angle 3.95888 ( 2811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7790 (mt) cc_final: 0.7337 (pt) REVERT: A 425 CYS cc_start: 0.8304 (p) cc_final: 0.8092 (p) REVERT: A 463 MET cc_start: 0.8018 (mmm) cc_final: 0.7758 (mmt) REVERT: A 476 ILE cc_start: 0.9120 (mt) cc_final: 0.8698 (pt) REVERT: A 511 LYS cc_start: 0.7023 (mttp) cc_final: 0.6346 (tptt) REVERT: A 600 ILE cc_start: 0.9252 (mt) cc_final: 0.8937 (mm) REVERT: A 1063 TRP cc_start: 0.7758 (m100) cc_final: 0.7422 (m-10) REVERT: B 445 VAL cc_start: 0.6996 (p) cc_final: 0.6792 (t) REVERT: B 500 ILE cc_start: 0.9055 (mt) cc_final: 0.8742 (mm) REVERT: B 519 ASP cc_start: 0.8504 (m-30) cc_final: 0.8162 (t70) REVERT: B 585 MET cc_start: 0.8564 (mmm) cc_final: 0.8252 (mmm) REVERT: B 1008 GLN cc_start: 0.7245 (pt0) cc_final: 0.6905 (pt0) REVERT: B 1023 MET cc_start: 0.8699 (tpt) cc_final: 0.8082 (tpt) REVERT: B 1065 THR cc_start: 0.6980 (t) cc_final: 0.6100 (m) REVERT: B 1115 PHE cc_start: 0.7084 (t80) cc_final: 0.6434 (t80) REVERT: C 438 PHE cc_start: 0.6000 (p90) cc_final: 0.5339 (p90) REVERT: C 501 SER cc_start: 0.8107 (p) cc_final: 0.7826 (t) REVERT: C 817 LYS cc_start: 0.8102 (mmpt) cc_final: 0.7754 (mmmt) REVERT: C 1020 PHE cc_start: 0.8137 (t80) cc_final: 0.7844 (t80) REVERT: C 1031 TYR cc_start: 0.3978 (p90) cc_final: 0.3134 (p90) REVERT: C 1130 ARG cc_start: 0.7343 (tpm170) cc_final: 0.5735 (tpt90) REVERT: D 405 TYR cc_start: 0.7519 (m-80) cc_final: 0.7183 (m-80) REVERT: D 425 CYS cc_start: 0.7983 (m) cc_final: 0.7775 (m) REVERT: D 518 LEU cc_start: 0.8652 (mt) cc_final: 0.8234 (mt) REVERT: D 580 SER cc_start: 0.9350 (m) cc_final: 0.8775 (p) REVERT: D 647 TYR cc_start: 0.7621 (p90) cc_final: 0.7419 (p90) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.1213 time to fit residues: 84.9125 Evaluate side-chains 342 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 200 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 196 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1078 GLN D 435 HIS D 587 GLN ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN D1204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102822 restraints weight = 39481.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105281 restraints weight = 23700.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106947 restraints weight = 17268.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107964 restraints weight = 14176.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108298 restraints weight = 12564.199| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19239 Z= 0.136 Angle : 0.617 14.102 25999 Z= 0.316 Chirality : 0.041 0.242 2911 Planarity : 0.004 0.070 3188 Dihedral : 6.594 88.380 2697 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2362 helix: 1.59 (0.14), residues: 1308 sheet: -1.40 (0.44), residues: 142 loop : -1.73 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 594 TYR 0.023 0.001 TYR A 673 PHE 0.027 0.001 PHE C1200 TRP 0.025 0.002 TRP D 767 HIS 0.015 0.001 HIS D1059 Details of bonding type rmsd covalent geometry : bond 0.00314 (19227) covalent geometry : angle 0.61171 (25975) SS BOND : bond 0.01196 ( 12) SS BOND : angle 2.82903 ( 24) hydrogen bonds : bond 0.03477 ( 958) hydrogen bonds : angle 3.83714 ( 2811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7778 (mt) cc_final: 0.7368 (pt) REVERT: A 425 CYS cc_start: 0.8230 (p) cc_final: 0.7967 (p) REVERT: A 463 MET cc_start: 0.7948 (mmm) cc_final: 0.7713 (mmt) REVERT: A 511 LYS cc_start: 0.6962 (mttp) cc_final: 0.6336 (tptt) REVERT: A 600 ILE cc_start: 0.9193 (mt) cc_final: 0.8867 (mm) REVERT: A 670 MET cc_start: 0.7349 (mmt) cc_final: 0.7142 (mmt) REVERT: A 671 TRP cc_start: 0.7723 (t-100) cc_final: 0.7449 (t-100) REVERT: A 732 TYR cc_start: 0.8029 (m-10) cc_final: 0.7486 (m-80) REVERT: A 1063 TRP cc_start: 0.7707 (m100) cc_final: 0.7430 (m-10) REVERT: B 500 ILE cc_start: 0.9067 (mt) cc_final: 0.8740 (mm) REVERT: B 519 ASP cc_start: 0.8434 (m-30) cc_final: 0.8148 (t70) REVERT: B 585 MET cc_start: 0.8553 (mmm) cc_final: 0.8273 (mmm) REVERT: B 592 SER cc_start: 0.8217 (t) cc_final: 0.7950 (p) REVERT: B 655 THR cc_start: 0.6340 (t) cc_final: 0.5988 (t) REVERT: B 1008 GLN cc_start: 0.7228 (pt0) cc_final: 0.6827 (pt0) REVERT: B 1023 MET cc_start: 0.8712 (tpt) cc_final: 0.8235 (tpt) REVERT: B 1065 THR cc_start: 0.7037 (t) cc_final: 0.6115 (m) REVERT: B 1115 PHE cc_start: 0.7087 (t80) cc_final: 0.6384 (t80) REVERT: C 438 PHE cc_start: 0.5886 (p90) cc_final: 0.5225 (p90) REVERT: C 501 SER cc_start: 0.8181 (p) cc_final: 0.7937 (t) REVERT: C 817 LYS cc_start: 0.8054 (mmpt) cc_final: 0.7708 (mmmt) REVERT: C 1020 PHE cc_start: 0.8105 (t80) cc_final: 0.7793 (t80) REVERT: C 1031 TYR cc_start: 0.3679 (p90) cc_final: 0.2886 (p90) REVERT: C 1130 ARG cc_start: 0.7318 (tpm170) cc_final: 0.5659 (tpt90) REVERT: C 1156 ILE cc_start: 0.8637 (mt) cc_final: 0.8380 (mp) REVERT: D 405 TYR cc_start: 0.7449 (m-80) cc_final: 0.7169 (m-80) REVERT: D 425 CYS cc_start: 0.8111 (m) cc_final: 0.7806 (m) REVERT: D 476 ILE cc_start: 0.8859 (mt) cc_final: 0.8651 (mt) REVERT: D 518 LEU cc_start: 0.8578 (mt) cc_final: 0.8207 (mt) REVERT: D 580 SER cc_start: 0.9289 (m) cc_final: 0.8703 (p) REVERT: D 594 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8068 (ttp80) REVERT: D 644 GLU cc_start: 0.7058 (mp0) cc_final: 0.6460 (tm-30) REVERT: D 645 ILE cc_start: 0.7648 (mt) cc_final: 0.7395 (mt) REVERT: D 816 TYR cc_start: 0.6277 (t80) cc_final: 0.5993 (t80) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.1117 time to fit residues: 78.8733 Evaluate side-chains 347 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 98 optimal weight: 0.0870 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN D1081 HIS D1159 ASN D1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103424 restraints weight = 39436.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105953 restraints weight = 23890.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107608 restraints weight = 17394.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108442 restraints weight = 14315.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.109144 restraints weight = 12851.892| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19239 Z= 0.122 Angle : 0.599 14.012 25999 Z= 0.307 Chirality : 0.041 0.247 2911 Planarity : 0.004 0.060 3188 Dihedral : 6.389 84.138 2697 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2362 helix: 1.74 (0.15), residues: 1304 sheet: -1.50 (0.41), residues: 162 loop : -1.59 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 594 TYR 0.022 0.001 TYR D 647 PHE 0.027 0.001 PHE C1200 TRP 0.020 0.001 TRP D1177 HIS 0.007 0.001 HIS D1059 Details of bonding type rmsd covalent geometry : bond 0.00275 (19227) covalent geometry : angle 0.59608 (25975) SS BOND : bond 0.00701 ( 12) SS BOND : angle 2.10360 ( 24) hydrogen bonds : bond 0.03355 ( 958) hydrogen bonds : angle 3.78510 ( 2811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7713 (mt) cc_final: 0.7311 (pt) REVERT: A 425 CYS cc_start: 0.8219 (p) cc_final: 0.8001 (p) REVERT: A 476 ILE cc_start: 0.9037 (mt) cc_final: 0.8658 (pt) REVERT: A 511 LYS cc_start: 0.6957 (mttp) cc_final: 0.6342 (tptt) REVERT: A 629 MET cc_start: 0.3721 (mpp) cc_final: 0.3139 (tpt) REVERT: A 670 MET cc_start: 0.7383 (mmt) cc_final: 0.7153 (mmt) REVERT: A 705 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7084 (mt-10) REVERT: A 732 TYR cc_start: 0.7889 (m-10) cc_final: 0.7103 (m-80) REVERT: A 1063 TRP cc_start: 0.7694 (m100) cc_final: 0.7439 (m-10) REVERT: B 500 ILE cc_start: 0.9085 (mt) cc_final: 0.8763 (mm) REVERT: B 519 ASP cc_start: 0.8399 (m-30) cc_final: 0.8139 (t70) REVERT: B 585 MET cc_start: 0.8537 (mmm) cc_final: 0.8282 (mmm) REVERT: B 592 SER cc_start: 0.8143 (t) cc_final: 0.7875 (p) REVERT: B 670 MET cc_start: 0.7027 (mpp) cc_final: 0.6808 (mpp) REVERT: B 1008 GLN cc_start: 0.7260 (pt0) cc_final: 0.6843 (pt0) REVERT: B 1023 MET cc_start: 0.8677 (tpt) cc_final: 0.8178 (tpt) REVERT: B 1065 THR cc_start: 0.7014 (t) cc_final: 0.6051 (m) REVERT: B 1115 PHE cc_start: 0.7206 (t80) cc_final: 0.6504 (t80) REVERT: C 438 PHE cc_start: 0.5844 (p90) cc_final: 0.5151 (p90) REVERT: C 497 SER cc_start: 0.8408 (t) cc_final: 0.8037 (m) REVERT: C 501 SER cc_start: 0.8070 (p) cc_final: 0.7825 (t) REVERT: C 722 LYS cc_start: 0.8399 (tttm) cc_final: 0.8102 (ptmm) REVERT: C 817 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7715 (mmmt) REVERT: C 1020 PHE cc_start: 0.8082 (t80) cc_final: 0.7807 (t80) REVERT: C 1130 ARG cc_start: 0.7233 (tpm170) cc_final: 0.5610 (tpt90) REVERT: D 405 TYR cc_start: 0.7421 (m-80) cc_final: 0.7161 (m-80) REVERT: D 425 CYS cc_start: 0.8076 (m) cc_final: 0.7824 (m) REVERT: D 518 LEU cc_start: 0.8533 (mt) cc_final: 0.8313 (mt) REVERT: D 527 MET cc_start: 0.6703 (mmt) cc_final: 0.6433 (mtt) REVERT: D 580 SER cc_start: 0.9292 (m) cc_final: 0.8706 (p) REVERT: D 644 GLU cc_start: 0.7183 (mp0) cc_final: 0.6522 (tm-30) REVERT: D 645 ILE cc_start: 0.7599 (mt) cc_final: 0.7326 (mt) REVERT: D 649 THR cc_start: 0.8789 (p) cc_final: 0.8377 (t) REVERT: D 752 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7933 (ttmm) REVERT: D 772 GLU cc_start: 0.5760 (mp0) cc_final: 0.5124 (mp0) REVERT: D 1082 PHE cc_start: 0.4040 (p90) cc_final: 0.2997 (p90) REVERT: A 1301 GLU cc_start: 0.5875 (mm-30) cc_final: 0.5512 (mm-30) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.1176 time to fit residues: 84.3135 Evaluate side-chains 350 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 192 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1198 HIS B1159 ASN D1159 ASN D1204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104822 restraints weight = 39042.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107128 restraints weight = 24468.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108695 restraints weight = 18258.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109415 restraints weight = 15238.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110193 restraints weight = 13815.477| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19239 Z= 0.123 Angle : 0.607 14.251 25999 Z= 0.311 Chirality : 0.041 0.248 2911 Planarity : 0.004 0.057 3188 Dihedral : 6.277 82.028 2697 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.17), residues: 2362 helix: 1.80 (0.15), residues: 1300 sheet: -1.42 (0.43), residues: 153 loop : -1.58 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 594 TYR 0.020 0.001 TYR B1031 PHE 0.028 0.001 PHE C1200 TRP 0.024 0.001 TRP C1063 HIS 0.007 0.001 HIS D1059 Details of bonding type rmsd covalent geometry : bond 0.00281 (19227) covalent geometry : angle 0.60442 (25975) SS BOND : bond 0.00678 ( 12) SS BOND : angle 2.06345 ( 24) hydrogen bonds : bond 0.03395 ( 958) hydrogen bonds : angle 3.78820 ( 2811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7673 (mt) cc_final: 0.7332 (pt) REVERT: A 425 CYS cc_start: 0.8233 (p) cc_final: 0.7936 (p) REVERT: A 476 ILE cc_start: 0.9076 (mt) cc_final: 0.8715 (pt) REVERT: A 511 LYS cc_start: 0.6985 (mttp) cc_final: 0.6389 (tptt) REVERT: A 629 MET cc_start: 0.3727 (mpp) cc_final: 0.3092 (tpt) REVERT: A 705 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7155 (mt-10) REVERT: A 732 TYR cc_start: 0.7726 (m-10) cc_final: 0.7221 (m-80) REVERT: A 1063 TRP cc_start: 0.7679 (m100) cc_final: 0.7451 (m-10) REVERT: A 1131 HIS cc_start: 0.6952 (m-70) cc_final: 0.6710 (m-70) REVERT: B 500 ILE cc_start: 0.9100 (mt) cc_final: 0.8761 (mm) REVERT: B 519 ASP cc_start: 0.8398 (m-30) cc_final: 0.8146 (t70) REVERT: B 585 MET cc_start: 0.8541 (mmm) cc_final: 0.8302 (mmm) REVERT: B 592 SER cc_start: 0.8147 (t) cc_final: 0.7879 (p) REVERT: B 1008 GLN cc_start: 0.7277 (pt0) cc_final: 0.6875 (pt0) REVERT: B 1023 MET cc_start: 0.8697 (tpt) cc_final: 0.8220 (tpt) REVERT: B 1115 PHE cc_start: 0.7177 (t80) cc_final: 0.6478 (t80) REVERT: C 438 PHE cc_start: 0.5819 (p90) cc_final: 0.5094 (p90) REVERT: C 501 SER cc_start: 0.8120 (p) cc_final: 0.7819 (t) REVERT: C 817 LYS cc_start: 0.8054 (mmpt) cc_final: 0.7728 (mmmt) REVERT: C 1020 PHE cc_start: 0.8063 (t80) cc_final: 0.7791 (t80) REVERT: C 1130 ARG cc_start: 0.7190 (tpm170) cc_final: 0.5585 (tpt90) REVERT: D 405 TYR cc_start: 0.7397 (m-80) cc_final: 0.7185 (m-80) REVERT: D 425 CYS cc_start: 0.8132 (m) cc_final: 0.7874 (m) REVERT: D 541 PHE cc_start: 0.8157 (t80) cc_final: 0.7675 (t80) REVERT: D 580 SER cc_start: 0.9311 (m) cc_final: 0.8712 (p) REVERT: D 644 GLU cc_start: 0.7100 (mp0) cc_final: 0.6765 (tt0) REVERT: D 649 THR cc_start: 0.8750 (p) cc_final: 0.8393 (t) REVERT: D 752 LYS cc_start: 0.8073 (mtpp) cc_final: 0.7865 (ttmm) REVERT: D 772 GLU cc_start: 0.5749 (mp0) cc_final: 0.5140 (mp0) REVERT: A 1301 GLU cc_start: 0.5690 (mm-30) cc_final: 0.5311 (mm-30) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.1161 time to fit residues: 83.0463 Evaluate side-chains 349 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 217 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 ASN D 587 GLN D1081 HIS D1159 ASN D1204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.127770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102215 restraints weight = 39293.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104484 restraints weight = 24886.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105975 restraints weight = 18703.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106640 restraints weight = 15699.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106640 restraints weight = 14293.673| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19239 Z= 0.156 Angle : 0.645 14.671 25999 Z= 0.331 Chirality : 0.042 0.250 2911 Planarity : 0.004 0.091 3188 Dihedral : 6.389 81.579 2697 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2362 helix: 1.62 (0.14), residues: 1304 sheet: -1.56 (0.42), residues: 158 loop : -1.54 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 594 TYR 0.023 0.002 TYR B1031 PHE 0.029 0.002 PHE C1200 TRP 0.020 0.002 TRP B1032 HIS 0.005 0.001 HIS D1059 Details of bonding type rmsd covalent geometry : bond 0.00362 (19227) covalent geometry : angle 0.64173 (25975) SS BOND : bond 0.00719 ( 12) SS BOND : angle 2.20934 ( 24) hydrogen bonds : bond 0.03663 ( 958) hydrogen bonds : angle 3.95036 ( 2811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7763 (mt) cc_final: 0.7364 (pt) REVERT: A 425 CYS cc_start: 0.8198 (p) cc_final: 0.7875 (p) REVERT: A 511 LYS cc_start: 0.6983 (mttp) cc_final: 0.6353 (tptt) REVERT: A 600 ILE cc_start: 0.9219 (mt) cc_final: 0.8808 (mm) REVERT: A 629 MET cc_start: 0.3739 (mpp) cc_final: 0.3207 (tpt) REVERT: A 633 ILE cc_start: 0.7403 (mm) cc_final: 0.6771 (mm) REVERT: A 670 MET cc_start: 0.7144 (mmt) cc_final: 0.6933 (mmt) REVERT: A 704 LEU cc_start: 0.8708 (pt) cc_final: 0.8409 (pp) REVERT: A 705 GLU cc_start: 0.7681 (mt-10) cc_final: 0.6971 (mt-10) REVERT: A 732 TYR cc_start: 0.7959 (m-10) cc_final: 0.7435 (m-80) REVERT: A 770 LYS cc_start: 0.6301 (mmpt) cc_final: 0.6073 (mmmt) REVERT: A 789 LEU cc_start: 0.8613 (tp) cc_final: 0.8407 (tt) REVERT: A 1063 TRP cc_start: 0.7688 (m100) cc_final: 0.7416 (m-10) REVERT: A 1131 HIS cc_start: 0.6974 (m-70) cc_final: 0.6764 (m-70) REVERT: B 500 ILE cc_start: 0.9142 (mt) cc_final: 0.8740 (mm) REVERT: B 519 ASP cc_start: 0.8460 (m-30) cc_final: 0.8259 (t70) REVERT: B 537 SER cc_start: 0.9266 (m) cc_final: 0.9012 (t) REVERT: B 585 MET cc_start: 0.8613 (mmm) cc_final: 0.8298 (mmm) REVERT: B 592 SER cc_start: 0.8170 (t) cc_final: 0.7919 (p) REVERT: B 1008 GLN cc_start: 0.7250 (pt0) cc_final: 0.6873 (pt0) REVERT: B 1023 MET cc_start: 0.8677 (tpt) cc_final: 0.8150 (tpt) REVERT: B 1115 PHE cc_start: 0.7307 (t80) cc_final: 0.6699 (t80) REVERT: C 438 PHE cc_start: 0.5936 (p90) cc_final: 0.5325 (p90) REVERT: C 629 MET cc_start: 0.4226 (tmm) cc_final: 0.3934 (tmm) REVERT: C 817 LYS cc_start: 0.8073 (mmpt) cc_final: 0.7762 (mmmt) REVERT: C 1020 PHE cc_start: 0.8111 (t80) cc_final: 0.7834 (t80) REVERT: C 1130 ARG cc_start: 0.7120 (tpm170) cc_final: 0.5663 (tpt90) REVERT: D 405 TYR cc_start: 0.7412 (m-80) cc_final: 0.7188 (m-80) REVERT: D 425 CYS cc_start: 0.8052 (m) cc_final: 0.7795 (m) REVERT: D 580 SER cc_start: 0.9327 (m) cc_final: 0.8756 (p) REVERT: D 644 GLU cc_start: 0.7117 (mp0) cc_final: 0.6863 (tt0) REVERT: D 649 THR cc_start: 0.8865 (p) cc_final: 0.8447 (t) REVERT: D 752 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7875 (ttmm) REVERT: D 772 GLU cc_start: 0.5787 (mp0) cc_final: 0.4722 (mp0) REVERT: A 1301 GLU cc_start: 0.5603 (mm-30) cc_final: 0.5109 (mm-30) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.1186 time to fit residues: 82.7168 Evaluate side-chains 347 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 28 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 224 optimal weight: 0.6980 chunk 1 optimal weight: 0.0270 chunk 82 optimal weight: 0.0070 chunk 194 optimal weight: 0.7980 chunk 219 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1198 HIS B1159 ASN D1159 ASN D1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105560 restraints weight = 39288.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107905 restraints weight = 24506.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109408 restraints weight = 18268.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110122 restraints weight = 15313.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110865 restraints weight = 13903.203| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19239 Z= 0.113 Angle : 0.609 14.201 25999 Z= 0.308 Chirality : 0.040 0.256 2911 Planarity : 0.004 0.083 3188 Dihedral : 6.097 85.728 2697 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.18), residues: 2362 helix: 1.91 (0.15), residues: 1293 sheet: -1.54 (0.43), residues: 151 loop : -1.39 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 594 TYR 0.020 0.001 TYR A 533 PHE 0.029 0.001 PHE C1200 TRP 0.018 0.001 TRP D1177 HIS 0.007 0.001 HIS D1059 Details of bonding type rmsd covalent geometry : bond 0.00247 (19227) covalent geometry : angle 0.60536 (25975) SS BOND : bond 0.00657 ( 12) SS BOND : angle 2.17471 ( 24) hydrogen bonds : bond 0.03307 ( 958) hydrogen bonds : angle 3.73057 ( 2811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3070.56 seconds wall clock time: 54 minutes 22.99 seconds (3262.99 seconds total)