Starting phenix.real_space_refine on Sun Sep 13 03:40:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uw4_20917/09_2026/6uw4_20917.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uw4_20917/09_2026/6uw4_20917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uw4_20917/09_2026/6uw4_20917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uw4_20917/09_2026/6uw4_20917.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uw4_20917/09_2026/6uw4_20917.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uw4_20917/09_2026/6uw4_20917.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uw4_20917/09_2026/6uw4_20917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uw4_20917/09_2026/6uw4_20917.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 20 5.49 5 S 116 5.16 5 Na 1 4.78 5 C 13220 2.51 5 N 3280 2.21 5 O 3644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20281 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4923 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 12, 'TRANS': 590} Chain breaks: 4 Chain: "B" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4923 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 12, 'TRANS': 590} Chain breaks: 4 Chain: "C" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4923 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 12, 'TRANS': 590} Chain breaks: 4 Chain: "D" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4923 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 12, 'TRANS': 590} Chain breaks: 4 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 148 Unusual residues: {' NA': 1, '6OU': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'6OU:plan-1': 4} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 147 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'6OU:plan-1': 4} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 147 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'6OU:plan-1': 4} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 147 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'6OU:plan-1': 4} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 4.21, per 1000 atoms: 0.21 Number of scatterers: 20281 At special positions: 0 Unit cell: (130.9, 130.9, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 20 15.00 Na 1 11.00 O 3644 8.00 N 3280 7.00 C 13220 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: 1.63 Conformation dependent library (CDL) restraints added in 833.9 milliseconds 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 64.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.732A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.755A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.649A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 264 through 271 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.904A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.746A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 422 through 436 removed outlier: 4.376A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 462 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 484 through 506 Processing helix chain 'A' and resid 520 through 541 removed outlier: 3.571A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.758A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.507A pdb=" N TYR A 565 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 removed outlier: 3.927A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 608 removed outlier: 3.861A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.703A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 685 removed outlier: 3.745A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.590A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.731A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 removed outlier: 3.755A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 removed outlier: 3.649A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 236 Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.904A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.746A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 422 through 436 removed outlier: 4.376A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 462 Processing helix chain 'B' and resid 481 through 483 No H-bonds generated for 'chain 'B' and resid 481 through 483' Processing helix chain 'B' and resid 484 through 506 Processing helix chain 'B' and resid 520 through 541 removed outlier: 3.571A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.758A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.506A pdb=" N TYR B 565 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 removed outlier: 3.927A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.860A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 removed outlier: 3.704A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.745A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.590A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 removed outlier: 3.732A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.755A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 163 removed outlier: 3.649A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 236 Processing helix chain 'C' and resid 264 through 271 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.904A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.746A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 422 through 436 removed outlier: 4.375A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 462 Processing helix chain 'C' and resid 481 through 483 No H-bonds generated for 'chain 'C' and resid 481 through 483' Processing helix chain 'C' and resid 484 through 506 Processing helix chain 'C' and resid 520 through 541 removed outlier: 3.570A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.758A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.507A pdb=" N TYR C 565 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 removed outlier: 3.927A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.862A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.703A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 685 removed outlier: 3.745A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.590A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 removed outlier: 3.731A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 removed outlier: 3.755A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.649A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 236 Processing helix chain 'D' and resid 264 through 271 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.904A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.746A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 422 through 436 removed outlier: 4.376A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 462 Processing helix chain 'D' and resid 481 through 483 No H-bonds generated for 'chain 'D' and resid 481 through 483' Processing helix chain 'D' and resid 484 through 506 Processing helix chain 'D' and resid 520 through 541 removed outlier: 3.571A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.758A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 removed outlier: 3.506A pdb=" N TYR D 565 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 removed outlier: 3.927A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 608 removed outlier: 3.861A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 removed outlier: 3.703A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 685 removed outlier: 3.745A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.591A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 7.023A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 7.022A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 7.023A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 7.023A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2916 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: 3.91 Time building geometry restraints manager: 2.26 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: 6016 1.34 - 1.45: 3359 1.45 - 1.57: 10725 1.57 - 1.69: 344 1.69 - 1.81: 236 Bond restraints: 20680 Sorted by residual: bond pdb=" C16 6OU D 803 " pdb=" O18 6OU D 803 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C16 6OU B 803 " pdb=" O18 6OU B 803 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C16 6OU C 803 " pdb=" O18 6OU C 803 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C16 6OU A 803 " pdb=" O18 6OU A 803 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C16 6OU C 802 " pdb=" O18 6OU C 802 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.91e+01 ... (remaining 20675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 27215 3.20 - 6.40: 481 6.40 - 9.60: 100 9.60 - 12.80: 20 12.80 - 16.00: 28 Bond angle restraints: 27844 Sorted by residual: angle pdb=" C HIS A 150 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta sigma weight residual 121.54 132.17 -10.63 1.91e+00 2.74e-01 3.10e+01 angle pdb=" C HIS B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 132.16 -10.62 1.91e+00 2.74e-01 3.09e+01 angle pdb=" C HIS C 150 " pdb=" N ASP C 151 " pdb=" CA ASP C 151 " ideal model delta sigma weight residual 121.54 132.13 -10.59 1.91e+00 2.74e-01 3.08e+01 angle pdb=" C HIS D 150 " pdb=" N ASP D 151 " pdb=" CA ASP D 151 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" O22 6OU D 804 " pdb=" P23 6OU D 804 " pdb=" O26 6OU D 804 " ideal model delta sigma weight residual 93.95 109.95 -16.00 3.00e+00 1.11e-01 2.85e+01 ... (remaining 27839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.32: 11692 29.32 - 58.65: 484 58.65 - 87.97: 40 87.97 - 117.29: 4 117.29 - 146.62: 20 Dihedral angle restraints: 12240 sinusoidal: 5156 harmonic: 7084 Sorted by residual: dihedral pdb=" CA GLY C 718 " pdb=" C GLY C 718 " pdb=" N GLU C 719 " pdb=" CA GLU C 719 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA GLY A 718 " pdb=" C GLY A 718 " pdb=" N GLU A 719 " pdb=" CA GLU A 719 " ideal model delta harmonic sigma weight residual 180.00 -156.49 -23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA GLY D 718 " pdb=" C GLY D 718 " pdb=" N GLU D 719 " pdb=" CA GLU D 719 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 12237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 3020 0.123 - 0.246: 68 0.246 - 0.369: 4 0.369 - 0.491: 4 0.491 - 0.614: 16 Chirality restraints: 3112 Sorted by residual: chirality pdb=" C20 6OU C 801 " pdb=" C19 6OU C 801 " pdb=" C21 6OU C 801 " pdb=" O30 6OU C 801 " both_signs ideal model delta sigma weight residual False 2.35 2.96 -0.61 2.00e-01 2.50e+01 9.43e+00 chirality pdb=" C20 6OU B 801 " pdb=" C19 6OU B 801 " pdb=" C21 6OU B 801 " pdb=" O30 6OU B 801 " both_signs ideal model delta sigma weight residual False 2.35 2.96 -0.61 2.00e-01 2.50e+01 9.42e+00 chirality pdb=" C20 6OU D 801 " pdb=" C19 6OU D 801 " pdb=" C21 6OU D 801 " pdb=" O30 6OU D 801 " both_signs ideal model delta sigma weight residual False 2.35 2.96 -0.61 2.00e-01 2.50e+01 9.39e+00 ... (remaining 3109 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 343 " 0.037 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO D 344 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 344 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 344 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 343 " -0.037 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO B 344 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 344 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 344 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 343 " -0.037 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 344 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.031 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5731 2.80 - 3.33: 17679 3.33 - 3.85: 32540 3.85 - 4.38: 37712 4.38 - 4.90: 66325 Nonbonded interactions: 159987 Sorted by model distance: nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.280 3.040 nonbonded pdb=" OD1 ASN D 180 " pdb=" OG1 THR D 183 " model vdw 2.280 3.040 nonbonded pdb=" OD1 ASN C 180 " pdb=" OG1 THR C 183 " model vdw 2.280 3.040 nonbonded pdb=" OD1 ASN A 180 " pdb=" OG1 THR A 183 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR B 650 " pdb=" O LYS C 545 " model vdw 2.290 3.040 ... (remaining 159982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 117 through 805) 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 18.750 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.015 0.141 20680 Z= 0.731 Angle : 1.184 16.004 27844 Z= 0.543 Chirality : 0.066 0.614 3112 Planarity : 0.006 0.055 3416 Dihedral : 17.291 146.618 7640 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % 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: -4.45 (0.12), residues: 2372 helix: -2.70 (0.09), residues: 1504 sheet: -2.43 (0.49), residues: 64 loop : -3.18 (0.17), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 225 TYR 0.013 0.002 TYR B 260 PHE 0.015 0.002 PHE D 436 TRP 0.019 0.002 TRP D 739 HIS 0.011 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.01492 / 0.73 (20680) covalent geometry : angle 1.18398 / 0.54 (27844) hydrogen bonds : bond 0.16372 / 10.64 ( 984) hydrogen bonds : angle 6.30864 / 4.43 ( 2916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.671 Fit side-chains REVERT: A 173 MET cc_start: 0.9187 (mtt) cc_final: 0.8832 (mtt) REVERT: A 481 TRP cc_start: 0.5836 (t60) cc_final: 0.5486 (m100) REVERT: B 173 MET cc_start: 0.9180 (mtt) cc_final: 0.8861 (mtt) REVERT: B 481 TRP cc_start: 0.5765 (t60) cc_final: 0.5384 (m100) REVERT: C 173 MET cc_start: 0.9165 (mtt) cc_final: 0.8874 (mtt) REVERT: C 481 TRP cc_start: 0.5739 (t60) cc_final: 0.5422 (m100) REVERT: D 173 MET cc_start: 0.9166 (mtt) cc_final: 0.8823 (mtt) REVERT: D 481 TRP cc_start: 0.5904 (t60) cc_final: 0.5428 (m100) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1445 time to fit residues: 52.8119 Evaluate side-chains 177 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS A 430 HIS A 561 ASN A 646 GLN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 430 HIS B 561 ASN B 646 GLN C 143 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 HIS C 430 HIS C 561 ASN C 646 GLN D 143 GLN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS D 430 HIS D 561 ASN D 646 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084681 restraints weight = 38848.479| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.37 r_work: 0.3017 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20680 Z= 0.106 Angle : 0.544 8.223 27844 Z= 0.279 Chirality : 0.037 0.158 3112 Planarity : 0.004 0.038 3416 Dihedral : 13.782 111.525 2920 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.94 % Allowed : 11.44 % Favored : 87.62 % 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: -1.99 (0.16), residues: 2372 helix: -0.47 (0.12), residues: 1520 sheet: -2.22 (0.51), residues: 64 loop : -2.85 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 716 TYR 0.008 0.001 TYR D 260 PHE 0.018 0.001 PHE D 715 TRP 0.014 0.001 TRP D 739 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (20680) covalent geometry : angle 0.54389 / 0.28 (27844) hydrogen bonds : bond 0.03486 / 2.31 ( 984) hydrogen bonds : angle 3.58997 / 2.49 ( 2916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.720 Fit side-chains REVERT: A 144 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8471 (mm-30) REVERT: A 173 MET cc_start: 0.9249 (mtt) cc_final: 0.8997 (mtp) REVERT: A 420 LEU cc_start: 0.9311 (mt) cc_final: 0.9075 (mt) REVERT: A 481 TRP cc_start: 0.5860 (t60) cc_final: 0.5337 (m100) REVERT: A 561 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8872 (m-40) REVERT: B 173 MET cc_start: 0.9255 (mtt) cc_final: 0.8953 (mtp) REVERT: B 420 LEU cc_start: 0.9316 (mt) cc_final: 0.9067 (mt) REVERT: B 481 TRP cc_start: 0.5820 (t60) cc_final: 0.5365 (m100) REVERT: B 561 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.8802 (m-40) REVERT: C 144 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8565 (mm-30) REVERT: C 173 MET cc_start: 0.9255 (mtt) cc_final: 0.8972 (mtp) REVERT: C 431 MET cc_start: 0.9053 (mtt) cc_final: 0.8773 (mtt) REVERT: C 481 TRP cc_start: 0.5643 (t60) cc_final: 0.5206 (m100) REVERT: C 561 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8808 (m-40) REVERT: D 144 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8550 (mm-30) REVERT: D 173 MET cc_start: 0.9243 (mtt) cc_final: 0.8988 (mtp) REVERT: D 420 LEU cc_start: 0.9321 (mt) cc_final: 0.9094 (mt) REVERT: D 431 MET cc_start: 0.9053 (mtt) cc_final: 0.8785 (mtt) REVERT: D 481 TRP cc_start: 0.5826 (t60) cc_final: 0.5218 (m100) REVERT: D 561 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8807 (m-40) outliers start: 20 outliers final: 12 residues processed: 240 average time/residue: 0.1204 time to fit residues: 46.6807 Evaluate side-chains 209 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 561 ASN Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 561 ASN Chi-restraints excluded: chain D residue 588 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 92 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN D 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.083254 restraints weight = 38756.408| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.29 r_work: 0.2989 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20680 Z= 0.183 Angle : 0.595 8.342 27844 Z= 0.303 Chirality : 0.040 0.168 3112 Planarity : 0.003 0.035 3416 Dihedral : 12.996 107.452 2920 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.41 % Allowed : 12.71 % Favored : 85.88 % 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: -1.23 (0.16), residues: 2372 helix: 0.20 (0.13), residues: 1528 sheet: -1.95 (0.57), residues: 64 loop : -2.75 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 716 TYR 0.014 0.002 TYR A 260 PHE 0.014 0.001 PHE A 715 TRP 0.011 0.001 TRP D 739 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (20680) covalent geometry : angle 0.59505 / 0.30 (27844) hydrogen bonds : bond 0.03796 / 2.49 ( 984) hydrogen bonds : angle 3.54034 / 2.46 ( 2916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.664 Fit side-chains REVERT: A 144 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8533 (mm-30) REVERT: A 173 MET cc_start: 0.9242 (mtt) cc_final: 0.8988 (mtp) REVERT: A 420 LEU cc_start: 0.9285 (mt) cc_final: 0.9061 (mt) REVERT: A 481 TRP cc_start: 0.5858 (t60) cc_final: 0.5252 (m100) REVERT: B 144 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8638 (mm-30) REVERT: B 173 MET cc_start: 0.9245 (mtt) cc_final: 0.8955 (mtp) REVERT: B 420 LEU cc_start: 0.9283 (mt) cc_final: 0.9060 (mt) REVERT: B 481 TRP cc_start: 0.5892 (t60) cc_final: 0.5298 (m100) REVERT: C 144 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8635 (mm-30) REVERT: C 173 MET cc_start: 0.9252 (mtt) cc_final: 0.8973 (mtp) REVERT: C 481 TRP cc_start: 0.5722 (t60) cc_final: 0.5216 (m100) REVERT: D 144 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8599 (mm-30) REVERT: D 173 MET cc_start: 0.9242 (mtt) cc_final: 0.8972 (mtp) REVERT: D 420 LEU cc_start: 0.9297 (mt) cc_final: 0.9061 (mt) REVERT: D 481 TRP cc_start: 0.5689 (t60) cc_final: 0.5211 (m100) outliers start: 30 outliers final: 17 residues processed: 206 average time/residue: 0.1192 time to fit residues: 40.2442 Evaluate side-chains 201 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 553 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 50 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.110102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.085484 restraints weight = 38904.456| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.50 r_work: 0.3029 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20680 Z= 0.090 Angle : 0.516 8.734 27844 Z= 0.260 Chirality : 0.036 0.153 3112 Planarity : 0.003 0.032 3416 Dihedral : 11.455 103.894 2920 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.03 % Allowed : 13.65 % Favored : 85.32 % 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: -0.36 (0.17), residues: 2372 helix: 1.05 (0.14), residues: 1472 sheet: -1.77 (0.61), residues: 64 loop : -2.55 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 716 TYR 0.007 0.001 TYR A 594 PHE 0.005 0.001 PHE A 654 TRP 0.012 0.001 TRP D 739 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (20680) covalent geometry : angle 0.51638 / 0.26 (27844) hydrogen bonds : bond 0.02772 / 1.83 ( 984) hydrogen bonds : angle 3.30067 / 2.30 ( 2916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.703 Fit side-chains REVERT: A 144 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8678 (mm-30) REVERT: A 431 MET cc_start: 0.8966 (mtp) cc_final: 0.8706 (mtp) REVERT: A 450 PHE cc_start: 0.8124 (m-80) cc_final: 0.7618 (t80) REVERT: A 481 TRP cc_start: 0.5832 (t60) cc_final: 0.5164 (m100) REVERT: A 717 MET cc_start: 0.8564 (tmm) cc_final: 0.8324 (tmm) REVERT: B 144 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8623 (mm-30) REVERT: B 173 MET cc_start: 0.9177 (mtt) cc_final: 0.8955 (mtp) REVERT: B 450 PHE cc_start: 0.8130 (m-80) cc_final: 0.7621 (t80) REVERT: B 481 TRP cc_start: 0.5818 (t60) cc_final: 0.5218 (m100) REVERT: B 717 MET cc_start: 0.8571 (tmm) cc_final: 0.8195 (tmm) REVERT: C 144 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8691 (mm-30) REVERT: C 173 MET cc_start: 0.9166 (mtt) cc_final: 0.8950 (mtp) REVERT: C 481 TRP cc_start: 0.5680 (t60) cc_final: 0.5073 (m100) REVERT: C 717 MET cc_start: 0.8630 (tmm) cc_final: 0.8246 (tmm) REVERT: D 144 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8652 (mm-30) REVERT: D 420 LEU cc_start: 0.9273 (mt) cc_final: 0.9042 (mt) REVERT: D 450 PHE cc_start: 0.8060 (m-80) cc_final: 0.7631 (t80) REVERT: D 481 TRP cc_start: 0.5663 (t60) cc_final: 0.5072 (m100) REVERT: D 717 MET cc_start: 0.8624 (tmm) cc_final: 0.8211 (tmm) outliers start: 22 outliers final: 16 residues processed: 228 average time/residue: 0.1186 time to fit residues: 44.1063 Evaluate side-chains 217 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 588 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 183 optimal weight: 20.0000 chunk 13 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 118 optimal weight: 0.0060 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 HIS B 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.108437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.083733 restraints weight = 38869.487| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.35 r_work: 0.3000 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20680 Z= 0.120 Angle : 0.546 10.951 27844 Z= 0.273 Chirality : 0.038 0.179 3112 Planarity : 0.003 0.031 3416 Dihedral : 11.110 102.804 2920 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.50 % Allowed : 13.51 % Favored : 84.99 % 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: -0.22 (0.17), residues: 2372 helix: 1.09 (0.13), residues: 1536 sheet: -1.58 (0.63), residues: 64 loop : -2.63 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 716 TYR 0.009 0.001 TYR D 260 PHE 0.006 0.001 PHE D 506 TRP 0.009 0.001 TRP C 739 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (20680) covalent geometry : angle 0.54591 / 0.27 (27844) hydrogen bonds : bond 0.03128 / 2.05 ( 984) hydrogen bonds : angle 3.33868 / 2.33 ( 2916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.767 Fit side-chains REVERT: A 144 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8680 (mm-30) REVERT: A 450 PHE cc_start: 0.8135 (m-80) cc_final: 0.7622 (t80) REVERT: A 481 TRP cc_start: 0.5773 (t60) cc_final: 0.5122 (m100) REVERT: B 144 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8617 (mm-30) REVERT: B 173 MET cc_start: 0.9170 (mtt) cc_final: 0.8944 (mtp) REVERT: B 450 PHE cc_start: 0.8137 (m-80) cc_final: 0.7623 (t80) REVERT: B 481 TRP cc_start: 0.5857 (t60) cc_final: 0.5176 (m100) REVERT: C 144 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8638 (mm-30) REVERT: C 173 MET cc_start: 0.9170 (mtt) cc_final: 0.8937 (mtp) REVERT: C 481 TRP cc_start: 0.5625 (t60) cc_final: 0.5013 (m100) REVERT: D 144 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8650 (mm-30) REVERT: D 420 LEU cc_start: 0.9269 (mt) cc_final: 0.9058 (mt) REVERT: D 450 PHE cc_start: 0.8053 (m-80) cc_final: 0.7597 (t80) REVERT: D 481 TRP cc_start: 0.5625 (t60) cc_final: 0.5017 (m100) outliers start: 32 outliers final: 26 residues processed: 217 average time/residue: 0.1259 time to fit residues: 44.9637 Evaluate side-chains 216 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 27 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 HIS D 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081030 restraints weight = 38677.492| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.32 r_work: 0.2950 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20680 Z= 0.213 Angle : 0.633 11.105 27844 Z= 0.316 Chirality : 0.041 0.196 3112 Planarity : 0.003 0.032 3416 Dihedral : 11.406 105.316 2920 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.16 % Allowed : 13.60 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2372 helix: 0.77 (0.13), residues: 1568 sheet: -1.63 (0.63), residues: 64 loop : -2.54 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 716 TYR 0.014 0.002 TYR A 451 PHE 0.013 0.001 PHE D 715 TRP 0.009 0.001 TRP A 380 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (20680) covalent geometry : angle 0.63292 / 0.32 (27844) hydrogen bonds : bond 0.03836 / 2.52 ( 984) hydrogen bonds : angle 3.54681 / 2.48 ( 2916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.753 Fit side-chains REVERT: A 144 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8630 (mm-30) REVERT: A 481 TRP cc_start: 0.5777 (t60) cc_final: 0.5118 (m100) REVERT: A 677 MET cc_start: 0.8356 (mtm) cc_final: 0.7994 (mtm) REVERT: A 704 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: B 144 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8670 (mm-30) REVERT: B 173 MET cc_start: 0.9202 (mtt) cc_final: 0.8943 (mtp) REVERT: B 481 TRP cc_start: 0.5638 (t60) cc_final: 0.5146 (m100) REVERT: B 677 MET cc_start: 0.8332 (mtm) cc_final: 0.7967 (mtm) REVERT: B 704 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: C 144 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8668 (mm-30) REVERT: C 481 TRP cc_start: 0.5650 (t60) cc_final: 0.5029 (m100) REVERT: C 677 MET cc_start: 0.8306 (mtm) cc_final: 0.7933 (mtm) REVERT: C 704 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: D 144 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8653 (mm-30) REVERT: D 481 TRP cc_start: 0.5641 (t60) cc_final: 0.5023 (m100) REVERT: D 677 MET cc_start: 0.8330 (mtm) cc_final: 0.7963 (mtm) REVERT: D 704 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7994 (tt0) outliers start: 46 outliers final: 31 residues processed: 225 average time/residue: 0.1251 time to fit residues: 46.0268 Evaluate side-chains 222 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 56 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.107115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082468 restraints weight = 38853.146| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.34 r_work: 0.2974 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20680 Z= 0.144 Angle : 0.576 11.112 27844 Z= 0.288 Chirality : 0.039 0.205 3112 Planarity : 0.003 0.031 3416 Dihedral : 10.976 104.628 2920 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.74 % Allowed : 14.45 % Favored : 83.82 % 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 (0.17), residues: 2372 helix: 1.05 (0.13), residues: 1548 sheet: -1.64 (0.63), residues: 64 loop : -2.64 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 714 TYR 0.011 0.001 TYR D 260 PHE 0.008 0.001 PHE C 715 TRP 0.011 0.001 TRP B 739 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (20680) covalent geometry : angle 0.57604 / 0.29 (27844) hydrogen bonds : bond 0.03361 / 2.21 ( 984) hydrogen bonds : angle 3.44022 / 2.40 ( 2916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.824 Fit side-chains REVERT: A 144 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8589 (mm-30) REVERT: A 481 TRP cc_start: 0.5657 (t60) cc_final: 0.5052 (m100) REVERT: A 717 MET cc_start: 0.8531 (tmm) cc_final: 0.8221 (tmm) REVERT: B 144 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8661 (mm-30) REVERT: B 173 MET cc_start: 0.9193 (mtt) cc_final: 0.8952 (mtp) REVERT: B 481 TRP cc_start: 0.5648 (t60) cc_final: 0.5033 (m100) REVERT: B 717 MET cc_start: 0.8600 (tmm) cc_final: 0.8366 (tmm) REVERT: C 144 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8661 (mm-30) REVERT: C 431 MET cc_start: 0.9034 (mtp) cc_final: 0.8714 (mtt) REVERT: C 481 TRP cc_start: 0.5632 (t60) cc_final: 0.5017 (m100) REVERT: D 144 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8652 (mm-30) REVERT: D 481 TRP cc_start: 0.5626 (t60) cc_final: 0.5017 (m100) REVERT: D 717 MET cc_start: 0.8600 (tmm) cc_final: 0.8312 (tmm) outliers start: 37 outliers final: 31 residues processed: 216 average time/residue: 0.1294 time to fit residues: 45.6447 Evaluate side-chains 222 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 635 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 129 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 195 optimal weight: 0.7980 chunk 183 optimal weight: 20.0000 chunk 147 optimal weight: 0.7980 chunk 217 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.1980 chunk 3 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.105962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.081353 restraints weight = 38849.987| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.32 r_work: 0.2954 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20680 Z= 0.188 Angle : 0.609 10.941 27844 Z= 0.305 Chirality : 0.040 0.189 3112 Planarity : 0.003 0.031 3416 Dihedral : 11.130 104.968 2920 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.02 % Allowed : 14.17 % Favored : 83.82 % 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: -0.36 (0.17), residues: 2372 helix: 0.86 (0.13), residues: 1568 sheet: -1.66 (0.64), residues: 64 loop : -2.54 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 716 TYR 0.014 0.002 TYR A 260 PHE 0.011 0.001 PHE B 715 TRP 0.010 0.001 TRP A 380 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (20680) covalent geometry : angle 0.60878 / 0.31 (27844) hydrogen bonds : bond 0.03683 / 2.42 ( 984) hydrogen bonds : angle 3.52723 / 2.46 ( 2916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.762 Fit side-chains REVERT: A 144 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8657 (mm-30) REVERT: A 481 TRP cc_start: 0.5686 (t60) cc_final: 0.5042 (m100) REVERT: A 677 MET cc_start: 0.8294 (mtm) cc_final: 0.7878 (mtm) REVERT: A 704 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: B 144 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8685 (mm-30) REVERT: B 481 TRP cc_start: 0.5586 (t60) cc_final: 0.5055 (m100) REVERT: B 677 MET cc_start: 0.8289 (mtm) cc_final: 0.7890 (mtm) REVERT: B 704 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: C 144 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8653 (mm-30) REVERT: C 481 TRP cc_start: 0.5714 (t60) cc_final: 0.5048 (m100) REVERT: C 677 MET cc_start: 0.8280 (mtm) cc_final: 0.7903 (mtm) REVERT: C 704 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: D 144 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8666 (mm-30) REVERT: D 481 TRP cc_start: 0.5625 (t60) cc_final: 0.5013 (m100) REVERT: D 677 MET cc_start: 0.8267 (mtm) cc_final: 0.7887 (mtm) REVERT: D 704 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8003 (tt0) outliers start: 43 outliers final: 34 residues processed: 214 average time/residue: 0.1267 time to fit residues: 44.4594 Evaluate side-chains 220 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 134 optimal weight: 0.0030 chunk 44 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 229 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 30 optimal weight: 0.0070 chunk 230 optimal weight: 6.9990 overall best weight: 0.7612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 523 HIS B 523 HIS C 523 HIS D 523 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084865 restraints weight = 38673.416| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.34 r_work: 0.3021 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20680 Z= 0.093 Angle : 0.543 11.030 27844 Z= 0.269 Chirality : 0.037 0.213 3112 Planarity : 0.003 0.031 3416 Dihedral : 10.263 102.037 2920 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.08 % Allowed : 15.48 % Favored : 83.44 % 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: 0.06 (0.18), residues: 2372 helix: 1.33 (0.13), residues: 1536 sheet: -1.67 (0.63), residues: 64 loop : -2.58 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 716 TYR 0.008 0.001 TYR A 594 PHE 0.009 0.001 PHE D 715 TRP 0.014 0.001 TRP B 739 HIS 0.003 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (20680) covalent geometry : angle 0.54307 / 0.27 (27844) hydrogen bonds : bond 0.02814 / 1.86 ( 984) hydrogen bonds : angle 3.33379 / 2.33 ( 2916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 0.903 Fit side-chains REVERT: A 144 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8656 (mm-30) REVERT: A 450 PHE cc_start: 0.8151 (m-80) cc_final: 0.7567 (t80) REVERT: A 481 TRP cc_start: 0.5589 (t60) cc_final: 0.4993 (m100) REVERT: B 144 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8694 (mm-30) REVERT: B 450 PHE cc_start: 0.8135 (m-80) cc_final: 0.7626 (t80) REVERT: B 481 TRP cc_start: 0.5598 (t60) cc_final: 0.5003 (m100) REVERT: C 144 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8711 (mm-30) REVERT: C 481 TRP cc_start: 0.5748 (t60) cc_final: 0.5064 (m100) REVERT: D 144 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8684 (mm-30) REVERT: D 450 PHE cc_start: 0.8121 (m-80) cc_final: 0.7617 (t80) REVERT: D 481 TRP cc_start: 0.5664 (t60) cc_final: 0.5033 (m100) outliers start: 23 outliers final: 23 residues processed: 211 average time/residue: 0.1239 time to fit residues: 42.7877 Evaluate side-chains 218 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 117 optimal weight: 0.0470 chunk 203 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 147 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.109209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.084552 restraints weight = 39121.179| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.36 r_work: 0.3017 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20680 Z= 0.101 Angle : 0.547 11.235 27844 Z= 0.270 Chirality : 0.037 0.198 3112 Planarity : 0.003 0.031 3416 Dihedral : 9.915 98.544 2920 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.22 % Allowed : 15.38 % Favored : 83.40 % 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: 0.16 (0.18), residues: 2372 helix: 1.40 (0.13), residues: 1536 sheet: -1.55 (0.63), residues: 64 loop : -2.53 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 716 TYR 0.008 0.001 TYR A 594 PHE 0.007 0.001 PHE D 715 TRP 0.013 0.001 TRP B 739 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (20680) covalent geometry : angle 0.54684 / 0.27 (27844) hydrogen bonds : bond 0.02916 / 1.92 ( 984) hydrogen bonds : angle 3.31052 / 2.31 ( 2916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.787 Fit side-chains REVERT: A 144 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8701 (mm-30) REVERT: A 450 PHE cc_start: 0.8131 (m-80) cc_final: 0.7578 (t80) REVERT: A 481 TRP cc_start: 0.5550 (t60) cc_final: 0.5017 (m100) REVERT: B 144 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8692 (mm-30) REVERT: B 450 PHE cc_start: 0.8131 (m-80) cc_final: 0.7575 (t80) REVERT: B 481 TRP cc_start: 0.5607 (t60) cc_final: 0.5030 (m100) REVERT: C 144 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8681 (mm-30) REVERT: C 450 PHE cc_start: 0.8112 (m-80) cc_final: 0.7611 (t80) REVERT: C 481 TRP cc_start: 0.5715 (t60) cc_final: 0.5077 (m100) REVERT: D 144 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8631 (mm-30) REVERT: D 450 PHE cc_start: 0.8124 (m-80) cc_final: 0.7576 (t80) REVERT: D 481 TRP cc_start: 0.5729 (t60) cc_final: 0.5076 (m100) outliers start: 26 outliers final: 24 residues processed: 212 average time/residue: 0.1281 time to fit residues: 44.4939 Evaluate side-chains 216 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 147 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 205 optimal weight: 0.0870 chunk 188 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084778 restraints weight = 38707.202| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.34 r_work: 0.3021 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20680 Z= 0.102 Angle : 0.548 11.204 27844 Z= 0.270 Chirality : 0.037 0.200 3112 Planarity : 0.003 0.031 3416 Dihedral : 9.519 96.108 2920 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.22 % Allowed : 15.76 % Favored : 83.02 % 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: 0.20 (0.18), residues: 2372 helix: 1.43 (0.13), residues: 1536 sheet: -1.57 (0.63), residues: 64 loop : -2.50 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 716 TYR 0.008 0.001 TYR B 321 PHE 0.006 0.001 PHE B 715 TRP 0.012 0.001 TRP B 739 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (20680) covalent geometry : angle 0.54810 / 0.27 (27844) hydrogen bonds : bond 0.02869 / 1.88 ( 984) hydrogen bonds : angle 3.30357 / 2.30 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4059.76 seconds wall clock time: 70 minutes 33.05 seconds (4233.05 seconds total)