Starting phenix.real_space_refine on Thu Mar 5 05:32:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zjg_14747/03_2026/7zjg_14747.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zjg_14747/03_2026/7zjg_14747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zjg_14747/03_2026/7zjg_14747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zjg_14747/03_2026/7zjg_14747.map" model { file = "/net/cci-nas-00/data/ceres_data/7zjg_14747/03_2026/7zjg_14747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zjg_14747/03_2026/7zjg_14747.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12808 2.51 5 N 3256 2.21 5 O 3356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 19532 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4883 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 579} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4883 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 579} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4883 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 579} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4883 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 579} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 4.42, per 1000 atoms: 0.23 Number of scatterers: 19532 At special positions: 0 Unit cell: (132.02, 132.02, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3356 8.00 N 3256 7.00 C 12808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.77 Conformation dependent library (CDL) restraints added in 849.2 milliseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 68.7% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 76 through 81 removed outlier: 4.010A pdb=" N LEU A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 103 removed outlier: 3.826A pdb=" N GLU A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 removed outlier: 3.590A pdb=" N THR A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.525A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.594A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 removed outlier: 4.108A pdb=" N VAL A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.723A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.891A pdb=" N VAL A 373 " --> pdb=" O HIS A 370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 414 removed outlier: 5.054A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.955A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.170A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.616A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.174A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 561 removed outlier: 4.007A pdb=" N VAL A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 604 removed outlier: 3.853A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 647 removed outlier: 3.999A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 652 removed outlier: 4.246A pdb=" N VAL A 652 " --> pdb=" O VAL A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 673 removed outlier: 3.709A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 679 removed outlier: 6.126A pdb=" N TRP A 677 " --> pdb=" O GLY A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.567A pdb=" N GLU A 716 " --> pdb=" O TRP A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 87 through 103 removed outlier: 3.827A pdb=" N GLU B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.590A pdb=" N THR B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.526A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.594A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 184 removed outlier: 4.109A pdb=" N VAL B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.723A pdb=" N GLU B 289 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 290' Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.891A pdb=" N VAL B 373 " --> pdb=" O HIS B 370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 414 removed outlier: 5.055A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 470 through 492 removed outlier: 3.955A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.171A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.616A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 522 No H-bonds generated for 'chain 'B' and resid 520 through 522' Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.174A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 561 removed outlier: 4.007A pdb=" N VAL B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 604 removed outlier: 3.852A pdb=" N THR B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 647 removed outlier: 3.999A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 removed outlier: 4.246A pdb=" N VAL B 652 " --> pdb=" O VAL B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 673 removed outlier: 3.707A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 679 removed outlier: 6.125A pdb=" N TRP B 677 " --> pdb=" O GLY B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 removed outlier: 3.567A pdb=" N GLU B 716 " --> pdb=" O TRP B 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 87 through 103 removed outlier: 3.825A pdb=" N GLU C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 removed outlier: 3.590A pdb=" N THR C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 removed outlier: 3.525A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 126 " --> pdb=" O MET C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.594A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 removed outlier: 4.109A pdb=" N VAL C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.723A pdb=" N GLU C 289 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 286 through 290' Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 308 through 316 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.891A pdb=" N VAL C 373 " --> pdb=" O HIS C 370 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 414 removed outlier: 5.054A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 459 through 466 Processing helix chain 'C' and resid 467 through 469 No H-bonds generated for 'chain 'C' and resid 467 through 469' Processing helix chain 'C' and resid 470 through 492 removed outlier: 3.955A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.169A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.616A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 522 No H-bonds generated for 'chain 'C' and resid 520 through 522' Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.174A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 561 removed outlier: 4.007A pdb=" N VAL C 532 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 604 removed outlier: 3.853A pdb=" N THR C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 647 removed outlier: 3.999A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 652 removed outlier: 4.246A pdb=" N VAL C 652 " --> pdb=" O VAL C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 673 removed outlier: 3.708A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 679 removed outlier: 6.125A pdb=" N TRP C 677 " --> pdb=" O GLY C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 removed outlier: 3.566A pdb=" N GLU C 716 " --> pdb=" O TRP C 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 87 through 103 removed outlier: 3.825A pdb=" N GLU D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.591A pdb=" N THR D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.525A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 126 " --> pdb=" O MET D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 146 Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.594A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 4.108A pdb=" N VAL D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.724A pdb=" N GLU D 289 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 286 through 290' Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.890A pdb=" N VAL D 373 " --> pdb=" O HIS D 370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 374 " --> pdb=" O ARG D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 414 removed outlier: 5.054A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 459 through 466 Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 470 through 492 removed outlier: 3.954A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.170A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.613A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 522 No H-bonds generated for 'chain 'D' and resid 520 through 522' Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.174A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 561 removed outlier: 4.007A pdb=" N VAL D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 604 removed outlier: 3.853A pdb=" N THR D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 647 removed outlier: 3.999A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 652 removed outlier: 4.246A pdb=" N VAL D 652 " --> pdb=" O VAL D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 673 removed outlier: 3.708A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 679 removed outlier: 6.125A pdb=" N TRP D 677 " --> pdb=" O GLY D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 removed outlier: 3.566A pdb=" N GLU D 716 " --> pdb=" O TRP D 712 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 334 removed outlier: 6.005A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 333 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG A 702 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 691 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 331 through 334 removed outlier: 6.005A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP B 333 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B 702 " --> pdb=" O VAL B 691 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 691 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.005A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP C 333 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG C 702 " --> pdb=" O VAL C 691 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 691 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 331 through 334 removed outlier: 6.006A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TRP D 333 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG D 702 " --> pdb=" O VAL D 691 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 691 " --> pdb=" O ARG D 702 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 2.33 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: 6017 1.34 - 1.46: 3747 1.46 - 1.58: 10088 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 20024 Sorted by residual: bond pdb=" CA SER D 504 " pdb=" CB SER D 504 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.55e-02 4.16e+03 1.03e+01 bond pdb=" CA SER A 504 " pdb=" CB SER A 504 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.55e-02 4.16e+03 1.02e+01 bond pdb=" CA SER C 504 " pdb=" CB SER C 504 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.55e-02 4.16e+03 1.01e+01 bond pdb=" CA SER B 504 " pdb=" CB SER B 504 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.55e-02 4.16e+03 9.91e+00 bond pdb=" N ARG B 517 " pdb=" CA ARG B 517 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.33e-02 5.65e+03 6.89e+00 ... (remaining 20019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 26114 1.38 - 2.76: 713 2.76 - 4.14: 231 4.14 - 5.52: 58 5.52 - 6.91: 36 Bond angle restraints: 27152 Sorted by residual: angle pdb=" N SER D 504 " pdb=" CA SER D 504 " pdb=" C SER D 504 " ideal model delta sigma weight residual 111.07 107.15 3.92 1.07e+00 8.73e-01 1.34e+01 angle pdb=" N SER A 504 " pdb=" CA SER A 504 " pdb=" C SER A 504 " ideal model delta sigma weight residual 111.07 107.16 3.91 1.07e+00 8.73e-01 1.34e+01 angle pdb=" N SER C 504 " pdb=" CA SER C 504 " pdb=" C SER C 504 " ideal model delta sigma weight residual 111.07 107.19 3.88 1.07e+00 8.73e-01 1.31e+01 angle pdb=" N SER B 504 " pdb=" CA SER B 504 " pdb=" C SER B 504 " ideal model delta sigma weight residual 111.07 107.19 3.88 1.07e+00 8.73e-01 1.31e+01 angle pdb=" CA LEU D 99 " pdb=" C LEU D 99 " pdb=" O LEU D 99 " ideal model delta sigma weight residual 121.84 117.77 4.07 1.16e+00 7.43e-01 1.23e+01 ... (remaining 27147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.68: 10357 14.68 - 29.36: 978 29.36 - 44.04: 350 44.04 - 58.72: 51 58.72 - 73.40: 12 Dihedral angle restraints: 11748 sinusoidal: 4740 harmonic: 7008 Sorted by residual: dihedral pdb=" CA GLY B 608 " pdb=" C GLY B 608 " pdb=" N GLU B 609 " pdb=" CA GLU B 609 " ideal model delta harmonic sigma weight residual -180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY D 608 " pdb=" C GLY D 608 " pdb=" N GLU D 609 " pdb=" CA GLU D 609 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY A 608 " pdb=" C GLY A 608 " pdb=" N GLU A 609 " pdb=" CA GLU A 609 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2658 0.057 - 0.114: 388 0.114 - 0.171: 10 0.171 - 0.228: 0 0.228 - 0.285: 4 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CA ARG C 517 " pdb=" N ARG C 517 " pdb=" C ARG C 517 " pdb=" CB ARG C 517 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ARG B 517 " pdb=" N ARG B 517 " pdb=" C ARG B 517 " pdb=" CB ARG B 517 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ARG D 517 " pdb=" N ARG D 517 " pdb=" C ARG D 517 " pdb=" CB ARG D 517 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3057 not shown) Planarity restraints: 3340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 148 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO C 149 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 148 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 149 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 148 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO B 149 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 149 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 149 " 0.024 5.00e-02 4.00e+02 ... (remaining 3337 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3790 2.77 - 3.30: 20256 3.30 - 3.84: 31896 3.84 - 4.37: 35728 4.37 - 4.90: 61065 Nonbonded interactions: 152735 Sorted by model distance: nonbonded pdb=" O VAL D 153 " pdb=" OG SER D 166 " model vdw 2.241 3.040 nonbonded pdb=" O VAL C 153 " pdb=" OG SER C 166 " model vdw 2.242 3.040 nonbonded pdb=" O VAL B 153 " pdb=" OG SER B 166 " model vdw 2.242 3.040 nonbonded pdb=" O VAL A 153 " pdb=" OG SER A 166 " model vdw 2.243 3.040 nonbonded pdb=" O THR B 483 " pdb=" OG SER B 486 " model vdw 2.251 3.040 ... (remaining 152730 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.100 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 : 0.003 0.050 20024 Z= 0.147 Angle : 0.641 6.906 27152 Z= 0.332 Chirality : 0.039 0.285 3060 Planarity : 0.004 0.044 3340 Dihedral : 13.033 73.404 7220 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.33 % Favored : 91.33 % Rotamer: Outliers : 0.52 % Allowed : 0.05 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.18), residues: 2364 helix: 1.13 (0.14), residues: 1456 sheet: -0.40 (0.68), residues: 56 loop : -2.73 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 687 TYR 0.023 0.001 TYR B 471 PHE 0.010 0.001 PHE B 407 TRP 0.011 0.001 TRP D 715 HIS 0.003 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00261 (20024) covalent geometry : angle 0.64063 (27152) hydrogen bonds : bond 0.12218 ( 1048) hydrogen bonds : angle 4.92023 ( 3048) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 308 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.6171 (p90) cc_final: 0.5878 (p90) REVERT: D 623 LEU cc_start: 0.8682 (tt) cc_final: 0.8472 (mt) outliers start: 11 outliers final: 4 residues processed: 319 average time/residue: 0.1461 time to fit residues: 72.5638 Evaluate side-chains 258 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 254 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN A 413 HIS ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 413 HIS ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 413 HIS ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 413 HIS ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.156146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.113656 restraints weight = 38501.638| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.85 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20024 Z= 0.180 Angle : 0.659 7.900 27152 Z= 0.320 Chirality : 0.039 0.129 3060 Planarity : 0.004 0.042 3340 Dihedral : 4.451 54.135 2622 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.42 % Favored : 91.24 % Rotamer: Outliers : 1.32 % Allowed : 12.19 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.18), residues: 2364 helix: 1.38 (0.14), residues: 1448 sheet: -0.54 (0.71), residues: 56 loop : -2.48 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 687 TYR 0.031 0.002 TYR D 98 PHE 0.012 0.002 PHE C 705 TRP 0.018 0.001 TRP A 715 HIS 0.006 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00412 (20024) covalent geometry : angle 0.65854 (27152) hydrogen bonds : bond 0.03553 ( 1048) hydrogen bonds : angle 3.83939 ( 3048) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 276 average time/residue: 0.1307 time to fit residues: 57.3696 Evaluate side-chains 261 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 559 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 141 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 75 optimal weight: 0.0000 chunk 133 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.157273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.115049 restraints weight = 38511.641| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.84 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20024 Z= 0.135 Angle : 0.615 8.290 27152 Z= 0.295 Chirality : 0.037 0.133 3060 Planarity : 0.004 0.042 3340 Dihedral : 4.274 43.535 2622 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.08 % Favored : 91.58 % Rotamer: Outliers : 1.60 % Allowed : 15.77 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 2364 helix: 1.54 (0.14), residues: 1456 sheet: -0.73 (0.70), residues: 56 loop : -2.75 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 687 TYR 0.026 0.001 TYR A 335 PHE 0.018 0.001 PHE A 540 TRP 0.011 0.001 TRP D 715 HIS 0.004 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00307 (20024) covalent geometry : angle 0.61455 (27152) hydrogen bonds : bond 0.03133 ( 1048) hydrogen bonds : angle 3.58451 ( 3048) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 491 PHE cc_start: 0.7689 (m-80) cc_final: 0.7289 (m-80) REVERT: B 122 MET cc_start: 0.7653 (tmm) cc_final: 0.7329 (mtm) REVERT: B 126 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7519 (tt) REVERT: B 491 PHE cc_start: 0.7700 (m-80) cc_final: 0.7272 (m-80) REVERT: C 491 PHE cc_start: 0.7700 (m-80) cc_final: 0.7271 (m-80) REVERT: C 647 GLU cc_start: 0.8140 (pm20) cc_final: 0.7889 (pp20) REVERT: D 607 MET cc_start: 0.3174 (OUTLIER) cc_final: 0.2678 (mtm) REVERT: D 647 GLU cc_start: 0.8188 (pm20) cc_final: 0.7877 (pp20) outliers start: 34 outliers final: 17 residues processed: 280 average time/residue: 0.1380 time to fit residues: 60.4334 Evaluate side-chains 273 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 254 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 413 HIS Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 607 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 27 optimal weight: 10.0000 chunk 177 optimal weight: 30.0000 chunk 113 optimal weight: 2.9990 chunk 134 optimal weight: 0.0870 chunk 225 optimal weight: 0.8980 chunk 196 optimal weight: 0.6980 chunk 59 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 5 optimal weight: 0.0570 chunk 63 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 0.9478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 269 HIS ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS B 269 HIS C 169 HIS C 269 HIS ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 HIS D 269 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.158254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115662 restraints weight = 37941.836| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.86 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20024 Z= 0.117 Angle : 0.601 15.467 27152 Z= 0.286 Chirality : 0.036 0.142 3060 Planarity : 0.004 0.041 3340 Dihedral : 3.830 18.224 2608 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.63 % Favored : 91.03 % Rotamer: Outliers : 1.74 % Allowed : 17.56 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.18), residues: 2364 helix: 1.75 (0.14), residues: 1440 sheet: -1.03 (0.67), residues: 56 loop : -2.63 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 687 TYR 0.026 0.001 TYR C 98 PHE 0.016 0.001 PHE B 547 TRP 0.010 0.001 TRP D 715 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00262 (20024) covalent geometry : angle 0.60082 (27152) hydrogen bonds : bond 0.02922 ( 1048) hydrogen bonds : angle 3.45191 ( 3048) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7711 (tt) REVERT: A 491 PHE cc_start: 0.7796 (m-80) cc_final: 0.7452 (m-80) REVERT: B 122 MET cc_start: 0.7598 (tmm) cc_final: 0.7345 (mtm) REVERT: B 126 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7653 (tt) REVERT: B 491 PHE cc_start: 0.7781 (m-80) cc_final: 0.7447 (m-80) REVERT: C 122 MET cc_start: 0.7697 (mtm) cc_final: 0.7361 (mtm) REVERT: C 126 LEU cc_start: 0.7970 (pp) cc_final: 0.7671 (tt) REVERT: C 491 PHE cc_start: 0.7800 (m-80) cc_final: 0.7459 (m-80) REVERT: D 491 PHE cc_start: 0.7745 (m-80) cc_final: 0.7335 (m-80) REVERT: D 591 ARG cc_start: 0.6610 (mmp80) cc_final: 0.6335 (mmp80) outliers start: 37 outliers final: 23 residues processed: 289 average time/residue: 0.1355 time to fit residues: 61.8495 Evaluate side-chains 279 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 413 HIS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 413 HIS Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 644 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 138 optimal weight: 0.6980 chunk 204 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 218 optimal weight: 0.0970 chunk 146 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.158754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116181 restraints weight = 38046.235| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.88 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20024 Z= 0.115 Angle : 0.602 10.223 27152 Z= 0.287 Chirality : 0.036 0.141 3060 Planarity : 0.004 0.041 3340 Dihedral : 3.809 17.934 2608 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.38 % Favored : 91.29 % Rotamer: Outliers : 2.68 % Allowed : 17.89 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2364 helix: 1.86 (0.14), residues: 1416 sheet: -1.12 (0.67), residues: 56 loop : -2.25 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 687 TYR 0.012 0.001 TYR A 335 PHE 0.016 0.001 PHE B 547 TRP 0.009 0.001 TRP D 715 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00257 (20024) covalent geometry : angle 0.60236 (27152) hydrogen bonds : bond 0.02916 ( 1048) hydrogen bonds : angle 3.41850 ( 3048) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.3215 (OUTLIER) cc_final: 0.2824 (pmm) REVERT: A 491 PHE cc_start: 0.7961 (m-80) cc_final: 0.7724 (m-80) REVERT: A 637 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9088 (tp) REVERT: B 122 MET cc_start: 0.7627 (tmm) cc_final: 0.7394 (mtm) REVERT: B 126 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7622 (tt) REVERT: B 137 MET cc_start: 0.3264 (OUTLIER) cc_final: 0.2920 (pmm) REVERT: B 491 PHE cc_start: 0.7948 (m-80) cc_final: 0.7689 (m-80) REVERT: B 637 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9071 (tp) REVERT: B 645 MET cc_start: 0.8749 (tmm) cc_final: 0.8458 (mmt) REVERT: C 137 MET cc_start: 0.3287 (OUTLIER) cc_final: 0.2924 (pmm) REVERT: C 491 PHE cc_start: 0.7966 (m-80) cc_final: 0.7729 (m-80) REVERT: C 637 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9085 (tp) REVERT: D 491 PHE cc_start: 0.7856 (m-80) cc_final: 0.7515 (m-80) REVERT: D 591 ARG cc_start: 0.6736 (mmp80) cc_final: 0.6408 (mmp80) REVERT: D 640 MET cc_start: 0.8287 (mmp) cc_final: 0.7951 (tpp) outliers start: 57 outliers final: 32 residues processed: 306 average time/residue: 0.1382 time to fit residues: 67.7147 Evaluate side-chains 287 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 248 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 413 HIS Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 642 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 117 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 230 optimal weight: 20.0000 chunk 154 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.157541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115395 restraints weight = 37847.279| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.81 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20024 Z= 0.128 Angle : 0.629 16.041 27152 Z= 0.298 Chirality : 0.037 0.143 3060 Planarity : 0.004 0.042 3340 Dihedral : 3.853 18.045 2608 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.16 % Favored : 91.50 % Rotamer: Outliers : 2.31 % Allowed : 21.19 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 2364 helix: 1.64 (0.14), residues: 1452 sheet: -1.19 (0.67), residues: 56 loop : -2.52 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 687 TYR 0.029 0.001 TYR D 98 PHE 0.019 0.001 PHE D 540 TRP 0.010 0.001 TRP D 715 HIS 0.005 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00292 (20024) covalent geometry : angle 0.62905 (27152) hydrogen bonds : bond 0.02965 ( 1048) hydrogen bonds : angle 3.48624 ( 3048) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.3350 (OUTLIER) cc_final: 0.2892 (pmm) REVERT: A 605 ILE cc_start: 0.1022 (OUTLIER) cc_final: 0.0412 (pt) REVERT: B 137 MET cc_start: 0.3360 (OUTLIER) cc_final: 0.2981 (pmm) REVERT: B 491 PHE cc_start: 0.7977 (m-80) cc_final: 0.7773 (m-80) REVERT: C 122 MET cc_start: 0.7840 (tmm) cc_final: 0.7621 (tmm) REVERT: C 137 MET cc_start: 0.3503 (OUTLIER) cc_final: 0.3051 (pmm) REVERT: C 491 PHE cc_start: 0.7946 (m-80) cc_final: 0.7745 (m-80) REVERT: D 137 MET cc_start: 0.3637 (OUTLIER) cc_final: 0.3156 (pmm) REVERT: D 491 PHE cc_start: 0.7918 (m-80) cc_final: 0.7665 (m-80) REVERT: D 591 ARG cc_start: 0.6778 (mmp80) cc_final: 0.6535 (mmp80) REVERT: D 645 MET cc_start: 0.8772 (tmm) cc_final: 0.8475 (tmm) outliers start: 49 outliers final: 27 residues processed: 292 average time/residue: 0.1421 time to fit residues: 65.1081 Evaluate side-chains 288 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 413 HIS Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 605 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 39 optimal weight: 4.9990 chunk 130 optimal weight: 0.0050 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 156 GLN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 156 GLN C 133 ASN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.155460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.113028 restraints weight = 37821.877| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.79 r_work: 0.3435 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20024 Z= 0.155 Angle : 0.657 14.006 27152 Z= 0.314 Chirality : 0.038 0.199 3060 Planarity : 0.004 0.045 3340 Dihedral : 4.001 18.757 2608 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.88 % Favored : 90.95 % Rotamer: Outliers : 2.35 % Allowed : 21.80 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2364 helix: 1.60 (0.14), residues: 1424 sheet: -1.24 (0.69), residues: 56 loop : -2.26 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 687 TYR 0.008 0.001 TYR B 228 PHE 0.021 0.001 PHE B 547 TRP 0.011 0.001 TRP B 715 HIS 0.006 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00357 (20024) covalent geometry : angle 0.65677 (27152) hydrogen bonds : bond 0.03176 ( 1048) hydrogen bonds : angle 3.59972 ( 3048) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.3796 (OUTLIER) cc_final: 0.3245 (pmm) REVERT: A 473 GLU cc_start: 0.8096 (tp30) cc_final: 0.7849 (mm-30) REVERT: A 605 ILE cc_start: 0.1334 (OUTLIER) cc_final: 0.0661 (pt) REVERT: A 669 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8486 (mm) REVERT: B 137 MET cc_start: 0.3846 (OUTLIER) cc_final: 0.3332 (pmm) REVERT: B 255 MET cc_start: 0.8610 (mtt) cc_final: 0.8399 (mtt) REVERT: B 473 GLU cc_start: 0.8090 (tp30) cc_final: 0.7842 (mm-30) REVERT: B 605 ILE cc_start: 0.1762 (OUTLIER) cc_final: 0.1059 (pt) REVERT: B 669 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8498 (mm) REVERT: C 122 MET cc_start: 0.8035 (tmm) cc_final: 0.7541 (tmm) REVERT: C 137 MET cc_start: 0.3851 (OUTLIER) cc_final: 0.3255 (pmm) REVERT: C 473 GLU cc_start: 0.8101 (tp30) cc_final: 0.7847 (mm-30) REVERT: C 605 ILE cc_start: 0.1716 (OUTLIER) cc_final: 0.0974 (pt) REVERT: C 669 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8470 (mm) REVERT: D 137 MET cc_start: 0.4128 (OUTLIER) cc_final: 0.3521 (pmm) REVERT: D 669 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8493 (mm) outliers start: 50 outliers final: 29 residues processed: 301 average time/residue: 0.1394 time to fit residues: 66.6465 Evaluate side-chains 293 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 84 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.157813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115597 restraints weight = 38044.341| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.84 r_work: 0.3471 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20024 Z= 0.115 Angle : 0.622 15.223 27152 Z= 0.297 Chirality : 0.037 0.142 3060 Planarity : 0.004 0.041 3340 Dihedral : 3.899 17.970 2608 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.46 % Favored : 91.37 % Rotamer: Outliers : 1.60 % Allowed : 22.60 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2364 helix: 1.55 (0.14), residues: 1452 sheet: -1.06 (0.72), residues: 56 loop : -2.45 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 687 TYR 0.031 0.001 TYR D 98 PHE 0.024 0.001 PHE B 547 TRP 0.009 0.001 TRP B 715 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00258 (20024) covalent geometry : angle 0.62194 (27152) hydrogen bonds : bond 0.02990 ( 1048) hydrogen bonds : angle 3.51886 ( 3048) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.3662 (OUTLIER) cc_final: 0.3103 (pmm) REVERT: A 605 ILE cc_start: 0.1317 (OUTLIER) cc_final: 0.0802 (pt) REVERT: B 137 MET cc_start: 0.3732 (OUTLIER) cc_final: 0.3191 (pmm) REVERT: C 137 MET cc_start: 0.3852 (OUTLIER) cc_final: 0.3236 (pmm) REVERT: D 137 MET cc_start: 0.4056 (OUTLIER) cc_final: 0.3433 (pmm) REVERT: D 647 GLU cc_start: 0.8154 (pp20) cc_final: 0.7896 (pp20) outliers start: 34 outliers final: 25 residues processed: 294 average time/residue: 0.1379 time to fit residues: 64.4009 Evaluate side-chains 284 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 605 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 263 ASN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN C 156 GLN C 222 GLN ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN D 222 GLN ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.151147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.108413 restraints weight = 37870.278| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.77 r_work: 0.3362 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 20024 Z= 0.252 Angle : 0.770 17.807 27152 Z= 0.374 Chirality : 0.043 0.183 3060 Planarity : 0.005 0.052 3340 Dihedral : 4.536 20.826 2608 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.05 % Favored : 90.74 % Rotamer: Outliers : 2.40 % Allowed : 22.03 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2364 helix: 1.31 (0.14), residues: 1400 sheet: -1.09 (0.78), residues: 56 loop : -2.43 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 687 TYR 0.013 0.002 TYR D 400 PHE 0.030 0.002 PHE C 547 TRP 0.015 0.002 TRP D 715 HIS 0.007 0.002 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00581 (20024) covalent geometry : angle 0.76963 (27152) hydrogen bonds : bond 0.03808 ( 1048) hydrogen bonds : angle 4.00603 ( 3048) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.4058 (OUTLIER) cc_final: 0.3508 (pmm) REVERT: A 433 MET cc_start: 0.5910 (tmm) cc_final: 0.5669 (tmm) REVERT: A 473 GLU cc_start: 0.8280 (tp30) cc_final: 0.8023 (mm-30) REVERT: A 528 MET cc_start: 0.9096 (ppp) cc_final: 0.8596 (ppp) REVERT: A 605 ILE cc_start: 0.2427 (OUTLIER) cc_final: 0.1756 (pt) REVERT: A 647 GLU cc_start: 0.8140 (pp20) cc_final: 0.7765 (pp20) REVERT: A 669 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8623 (mm) REVERT: B 137 MET cc_start: 0.4257 (OUTLIER) cc_final: 0.3659 (pmm) REVERT: B 473 GLU cc_start: 0.8295 (tp30) cc_final: 0.8044 (mm-30) REVERT: B 528 MET cc_start: 0.9059 (ppp) cc_final: 0.8538 (ppp) REVERT: B 669 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8633 (mm) REVERT: C 137 MET cc_start: 0.4345 (OUTLIER) cc_final: 0.3735 (pmm) REVERT: C 433 MET cc_start: 0.5922 (tmm) cc_final: 0.5682 (tmm) REVERT: C 473 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8006 (mm-30) REVERT: C 528 MET cc_start: 0.9133 (ppp) cc_final: 0.8663 (ppp) REVERT: C 669 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8626 (mm) REVERT: D 137 MET cc_start: 0.4450 (OUTLIER) cc_final: 0.3833 (pmm) REVERT: D 473 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8042 (mm-30) REVERT: D 669 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8635 (mm) outliers start: 51 outliers final: 32 residues processed: 293 average time/residue: 0.1380 time to fit residues: 64.1581 Evaluate side-chains 287 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 75 optimal weight: 0.0570 chunk 107 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 210 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.157519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.118241 restraints weight = 37909.898| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 4.53 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20024 Z= 0.117 Angle : 0.667 16.217 27152 Z= 0.318 Chirality : 0.038 0.168 3060 Planarity : 0.004 0.041 3340 Dihedral : 4.147 18.743 2608 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.71 % Favored : 91.12 % Rotamer: Outliers : 1.41 % Allowed : 23.49 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2364 helix: 1.77 (0.15), residues: 1364 sheet: -1.35 (0.73), residues: 56 loop : -2.00 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 687 TYR 0.032 0.001 TYR D 98 PHE 0.028 0.001 PHE C 547 TRP 0.010 0.001 TRP D 715 HIS 0.002 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00259 (20024) covalent geometry : angle 0.66653 (27152) hydrogen bonds : bond 0.03169 ( 1048) hydrogen bonds : angle 3.66539 ( 3048) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 433 MET cc_start: 0.5762 (tmm) cc_final: 0.5450 (tmm) REVERT: C 433 MET cc_start: 0.5743 (tmm) cc_final: 0.5439 (tmm) REVERT: C 603 PHE cc_start: 0.7239 (m-80) cc_final: 0.6830 (m-80) REVERT: D 647 GLU cc_start: 0.7967 (pp20) cc_final: 0.7716 (pp20) outliers start: 30 outliers final: 24 residues processed: 307 average time/residue: 0.1299 time to fit residues: 64.3148 Evaluate side-chains 286 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 605 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 122 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 181 optimal weight: 0.2980 chunk 115 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 83 optimal weight: 0.0060 chunk 221 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.157056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.115600 restraints weight = 37659.035| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.76 r_work: 0.3472 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.455 20024 Z= 0.316 Angle : 0.972 65.550 27152 Z= 0.572 Chirality : 0.039 0.348 3060 Planarity : 0.007 0.250 3340 Dihedral : 4.154 18.699 2608 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.76 % Favored : 91.03 % Rotamer: Outliers : 1.41 % Allowed : 24.11 % Favored : 74.48 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 2364 helix: 1.79 (0.15), residues: 1364 sheet: -1.36 (0.73), residues: 56 loop : -1.99 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 687 TYR 0.024 0.001 TYR B 471 PHE 0.026 0.001 PHE C 547 TRP 0.062 0.002 TRP B 223 HIS 0.002 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00658 (20024) covalent geometry : angle 0.97187 (27152) hydrogen bonds : bond 0.03174 ( 1048) hydrogen bonds : angle 3.66558 ( 3048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4115.04 seconds wall clock time: 71 minutes 59.30 seconds (4319.30 seconds total)