Starting phenix.real_space_refine on Thu Mar 5 07:53:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uw4_20917/03_2026/6uw4_20917.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uw4_20917/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6uw4_20917/03_2026/6uw4_20917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uw4_20917/03_2026/6uw4_20917.map" model { file = "/net/cci-nas-00/data/ceres_data/6uw4_20917/03_2026/6uw4_20917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uw4_20917/03_2026/6uw4_20917.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.91, per 1000 atoms: 0.24 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: 1.46 Conformation dependent library (CDL) restraints added in 964.3 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: 0.60 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: 3.15 Time building geometry restraints manager: 1.95 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 - 35.01: 11970 35.01 - 70.01: 378 70.01 - 105.02: 56 105.02 - 140.03: 24 140.03 - 175.04: 32 Dihedral angle restraints: 12460 sinusoidal: 5376 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 12457 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: 1.360 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.220 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 21.428 175.036 7860 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 covalent geometry : bond 0.01492 (20680) covalent geometry : angle 1.18398 (27844) hydrogen bonds : bond 0.16372 ( 984) hydrogen bonds : angle 6.30864 ( 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 : 0.744 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: 0.1625 time to fit residues: 59.0349 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 : 0.754 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS A 561 ASN A 646 GLN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 561 ASN B 646 GLN C 143 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 HIS C 561 ASN C 646 GLN D 143 GLN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS D 561 ASN D 646 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.084832 restraints weight = 38759.103| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.37 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: 0.8394 moved from start: 0.1563 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= 0.108 Angle : 0.551 8.105 27844 Z= 0.279 Chirality : 0.038 0.226 3112 Planarity : 0.004 0.038 3416 Dihedral : 21.077 170.078 3140 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.89 % Allowed : 11.54 % Favored : 87.57 % 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: -1.95 (0.16), residues: 2372 helix: -0.44 (0.12), residues: 1520 sheet: -2.20 (0.52), residues: 64 loop : -2.84 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 716 TYR 0.008 0.001 TYR D 260 PHE 0.019 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 covalent geometry : bond 0.00236 (20680) covalent geometry : angle 0.55076 (27844) hydrogen bonds : bond 0.03387 ( 984) hydrogen bonds : angle 3.55804 ( 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 250 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.710 Fit side-chains REVERT: A 144 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8490 (mm-30) REVERT: A 173 MET cc_start: 0.9242 (mtt) cc_final: 0.8985 (mtp) REVERT: A 420 LEU cc_start: 0.9313 (mt) cc_final: 0.9072 (mt) REVERT: A 481 TRP cc_start: 0.5912 (t60) cc_final: 0.5334 (m100) REVERT: A 561 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8873 (m-40) REVERT: B 144 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8599 (mm-30) REVERT: B 173 MET cc_start: 0.9257 (mtt) cc_final: 0.8954 (mtp) REVERT: B 420 LEU cc_start: 0.9314 (mt) cc_final: 0.9063 (mt) REVERT: B 431 MET cc_start: 0.9092 (mtt) cc_final: 0.8868 (mtt) REVERT: B 481 TRP cc_start: 0.5827 (t60) cc_final: 0.5366 (m100) REVERT: B 561 ASN cc_start: 0.9159 (OUTLIER) cc_final: 0.8802 (m-40) REVERT: C 144 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8588 (mm-30) REVERT: C 173 MET cc_start: 0.9260 (mtt) cc_final: 0.8989 (mtp) REVERT: C 431 MET cc_start: 0.9086 (mtt) cc_final: 0.8801 (mtt) REVERT: C 481 TRP cc_start: 0.5638 (t60) cc_final: 0.5202 (m100) REVERT: C 561 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8808 (m-40) REVERT: D 144 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8548 (mm-30) REVERT: D 173 MET cc_start: 0.9241 (mtt) cc_final: 0.8991 (mtp) REVERT: D 420 LEU cc_start: 0.9319 (mt) cc_final: 0.9091 (mt) REVERT: D 481 TRP cc_start: 0.5822 (t60) cc_final: 0.5213 (m100) REVERT: D 561 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8808 (m-40) outliers start: 19 outliers final: 11 residues processed: 245 average time/residue: 0.1303 time to fit residues: 51.2720 Evaluate side-chains 208 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 561 ASN Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 541 LEU 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 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: 8.9990 chunk 186 optimal weight: 0.1980 chunk 199 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3520 r_free = 0.3520 target = 0.107017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.082542 restraints weight = 38818.583| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.30 r_work: 0.2978 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20680 Z= 0.205 Angle : 0.620 8.513 27844 Z= 0.313 Chirality : 0.042 0.259 3112 Planarity : 0.004 0.035 3416 Dihedral : 20.478 166.455 3140 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.31 % Allowed : 12.38 % Favored : 86.30 % 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: -1.29 (0.16), residues: 2372 helix: 0.12 (0.13), residues: 1548 sheet: -1.94 (0.57), residues: 64 loop : -2.78 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 716 TYR 0.015 0.002 TYR A 260 PHE 0.017 0.001 PHE C 715 TRP 0.011 0.001 TRP D 739 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00486 (20680) covalent geometry : angle 0.61976 (27844) hydrogen bonds : bond 0.03930 ( 984) hydrogen bonds : angle 3.56964 ( 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 217 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.753 Fit side-chains REVERT: A 144 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8540 (mm-30) REVERT: A 173 MET cc_start: 0.9242 (mtt) cc_final: 0.8983 (mtp) REVERT: A 420 LEU cc_start: 0.9291 (mt) cc_final: 0.9068 (mt) REVERT: A 481 TRP cc_start: 0.5858 (t60) cc_final: 0.5248 (m100) REVERT: B 173 MET cc_start: 0.9249 (mtt) cc_final: 0.8957 (mtp) REVERT: B 420 LEU cc_start: 0.9284 (mt) cc_final: 0.9055 (mt) REVERT: B 481 TRP cc_start: 0.5892 (t60) cc_final: 0.5294 (m100) REVERT: C 173 MET cc_start: 0.9259 (mtt) cc_final: 0.8980 (mtp) REVERT: C 481 TRP cc_start: 0.5716 (t60) cc_final: 0.5211 (m100) REVERT: D 144 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8639 (mm-30) REVERT: D 173 MET cc_start: 0.9232 (mtt) cc_final: 0.8971 (mtp) REVERT: D 420 LEU cc_start: 0.9297 (mt) cc_final: 0.9072 (mt) REVERT: D 481 TRP cc_start: 0.5707 (t60) cc_final: 0.5206 (m100) outliers start: 28 outliers final: 13 residues processed: 205 average time/residue: 0.1300 time to fit residues: 43.3896 Evaluate side-chains 194 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 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 C residue 263 GLU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 553 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: 4.9990 chunk 129 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.0000 chunk 44 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.109087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084822 restraints weight = 38770.784| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.34 r_work: 0.3021 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2078 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= 0.098 Angle : 0.536 8.814 27844 Z= 0.268 Chirality : 0.038 0.249 3112 Planarity : 0.003 0.033 3416 Dihedral : 18.807 158.682 3140 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.98 % Allowed : 13.60 % Favored : 85.41 % 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: -0.52 (0.17), residues: 2372 helix: 0.88 (0.13), residues: 1512 sheet: -1.80 (0.61), residues: 64 loop : -2.68 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 716 TYR 0.007 0.001 TYR A 594 PHE 0.011 0.001 PHE D 715 TRP 0.012 0.001 TRP C 739 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00219 (20680) covalent geometry : angle 0.53632 (27844) hydrogen bonds : bond 0.02918 ( 984) hydrogen bonds : angle 3.34876 ( 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 219 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.796 Fit side-chains REVERT: A 144 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8661 (mm-30) REVERT: A 420 LEU cc_start: 0.9269 (mt) cc_final: 0.9041 (mt) REVERT: A 450 PHE cc_start: 0.8075 (m-80) cc_final: 0.7600 (t80) REVERT: A 481 TRP cc_start: 0.5868 (t60) cc_final: 0.5189 (m100) REVERT: A 717 MET cc_start: 0.8487 (tmm) cc_final: 0.8185 (tmm) REVERT: B 144 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8610 (mm-30) REVERT: B 173 MET cc_start: 0.9188 (mtt) cc_final: 0.8956 (mtp) REVERT: B 420 LEU cc_start: 0.9258 (mt) cc_final: 0.9032 (mt) REVERT: B 481 TRP cc_start: 0.5858 (t60) cc_final: 0.5229 (m100) REVERT: B 717 MET cc_start: 0.8481 (tmm) cc_final: 0.8189 (tmm) REVERT: C 144 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8649 (mm-30) REVERT: C 173 MET cc_start: 0.9189 (mtt) cc_final: 0.8966 (mtp) REVERT: C 481 TRP cc_start: 0.5643 (t60) cc_final: 0.5125 (m100) REVERT: C 717 MET cc_start: 0.8459 (tmm) cc_final: 0.8197 (tmm) REVERT: D 144 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8629 (mm-30) REVERT: D 173 MET cc_start: 0.9166 (mtt) cc_final: 0.8964 (mtp) REVERT: D 420 LEU cc_start: 0.9281 (mt) cc_final: 0.9048 (mt) REVERT: D 481 TRP cc_start: 0.5694 (t60) cc_final: 0.5090 (m100) REVERT: D 717 MET cc_start: 0.8568 (tmm) cc_final: 0.8203 (tmm) outliers start: 21 outliers final: 16 residues processed: 212 average time/residue: 0.1353 time to fit residues: 46.8773 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 : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 579 ILE 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: 9.9990 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 118 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082174 restraints weight = 38800.409| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.34 r_work: 0.2969 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20680 Z= 0.154 Angle : 0.577 10.479 27844 Z= 0.289 Chirality : 0.040 0.242 3112 Planarity : 0.003 0.033 3416 Dihedral : 18.779 160.040 3140 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.41 % Allowed : 13.70 % Favored : 84.90 % 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: -0.39 (0.17), residues: 2372 helix: 0.95 (0.13), residues: 1536 sheet: -1.62 (0.63), residues: 64 loop : -2.70 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 716 TYR 0.012 0.001 TYR B 260 PHE 0.007 0.001 PHE C 377 TRP 0.009 0.001 TRP B 739 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00366 (20680) covalent geometry : angle 0.57747 (27844) hydrogen bonds : bond 0.03467 ( 984) hydrogen bonds : angle 3.44147 ( 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 223 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.776 Fit side-chains REVERT: A 144 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8617 (mm-30) REVERT: A 420 LEU cc_start: 0.9274 (mt) cc_final: 0.9072 (mt) REVERT: A 481 TRP cc_start: 0.5796 (t60) cc_final: 0.5131 (m100) REVERT: B 144 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8622 (mm-30) REVERT: B 173 MET cc_start: 0.9203 (mtt) cc_final: 0.8959 (mtp) REVERT: B 481 TRP cc_start: 0.5641 (t60) cc_final: 0.5172 (m100) REVERT: B 677 MET cc_start: 0.8212 (mtm) cc_final: 0.7856 (mtm) REVERT: C 144 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8643 (mm-30) REVERT: C 173 MET cc_start: 0.9209 (mtt) cc_final: 0.8945 (mtp) REVERT: C 481 TRP cc_start: 0.5648 (t60) cc_final: 0.5024 (m100) REVERT: C 677 MET cc_start: 0.8226 (mtm) cc_final: 0.7856 (mtm) REVERT: D 144 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8629 (mm-30) REVERT: D 173 MET cc_start: 0.9201 (mtt) cc_final: 0.8966 (mtp) REVERT: D 481 TRP cc_start: 0.5641 (t60) cc_final: 0.5018 (m100) outliers start: 30 outliers final: 29 residues processed: 213 average time/residue: 0.1300 time to fit residues: 45.6313 Evaluate side-chains 214 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 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 398 THR Chi-restraints excluded: chain B residue 588 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 398 THR 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 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 398 THR 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: 0.1980 chunk 218 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 203 optimal weight: 0.0570 chunk 65 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 0.0970 chunk 178 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 overall best weight: 0.8698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3561 r_free = 0.3561 target = 0.109521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.085139 restraints weight = 38505.800| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.34 r_work: 0.3029 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20680 Z= 0.095 Angle : 0.542 11.639 27844 Z= 0.267 Chirality : 0.038 0.207 3112 Planarity : 0.003 0.033 3416 Dihedral : 17.774 158.430 3140 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.74 % Allowed : 14.12 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.04 (0.17), residues: 2372 helix: 1.32 (0.13), residues: 1512 sheet: -1.55 (0.63), residues: 64 loop : -2.47 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 716 TYR 0.007 0.001 TYR C 321 PHE 0.005 0.001 PHE D 715 TRP 0.012 0.001 TRP C 739 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00210 (20680) covalent geometry : angle 0.54232 (27844) hydrogen bonds : bond 0.02788 ( 984) hydrogen bonds : angle 3.30229 ( 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 239 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.784 Fit side-chains REVERT: A 144 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8677 (mm-30) REVERT: A 450 PHE cc_start: 0.8128 (m-80) cc_final: 0.7562 (t80) REVERT: A 481 TRP cc_start: 0.5617 (t60) cc_final: 0.5019 (m100) REVERT: B 144 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8655 (mm-30) REVERT: B 173 MET cc_start: 0.9137 (mtt) cc_final: 0.8933 (mtp) REVERT: B 450 PHE cc_start: 0.8137 (m-80) cc_final: 0.7573 (t80) REVERT: B 481 TRP cc_start: 0.5590 (t60) cc_final: 0.5049 (m100) REVERT: C 144 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8665 (mm-30) REVERT: C 173 MET cc_start: 0.9128 (mtt) cc_final: 0.8916 (mtp) REVERT: C 450 PHE cc_start: 0.8133 (m-80) cc_final: 0.7613 (t80) REVERT: C 481 TRP cc_start: 0.5600 (t60) cc_final: 0.5001 (m100) REVERT: D 144 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8692 (mm-30) REVERT: D 450 PHE cc_start: 0.8104 (m-80) cc_final: 0.7609 (t80) REVERT: D 481 TRP cc_start: 0.5583 (t60) cc_final: 0.4994 (m100) outliers start: 37 outliers final: 30 residues processed: 230 average time/residue: 0.1301 time to fit residues: 49.0844 Evaluate side-chains 226 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 398 THR 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 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 C residue 635 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 398 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 56 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 222 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.082090 restraints weight = 38843.884| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.33 r_work: 0.2968 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20680 Z= 0.168 Angle : 0.597 11.527 27844 Z= 0.295 Chirality : 0.040 0.224 3112 Planarity : 0.003 0.032 3416 Dihedral : 18.104 159.615 3140 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.11 % Allowed : 14.02 % Favored : 83.86 % 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: -0.11 (0.17), residues: 2372 helix: 1.14 (0.13), residues: 1548 sheet: -1.56 (0.63), residues: 64 loop : -2.57 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 714 TYR 0.012 0.001 TYR A 260 PHE 0.011 0.001 PHE A 715 TRP 0.009 0.001 TRP B 380 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00400 (20680) covalent geometry : angle 0.59660 (27844) hydrogen bonds : bond 0.03454 ( 984) hydrogen bonds : angle 3.43062 ( 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 239 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 0.771 Fit side-chains REVERT: A 144 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8637 (mm-30) REVERT: A 481 TRP cc_start: 0.5645 (t60) cc_final: 0.5026 (m100) REVERT: A 677 MET cc_start: 0.8300 (mtm) cc_final: 0.7964 (mtm) REVERT: A 704 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: B 144 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8667 (mm-30) REVERT: B 173 MET cc_start: 0.9180 (mtt) cc_final: 0.8942 (mtp) REVERT: B 481 TRP cc_start: 0.5619 (t60) cc_final: 0.5018 (m100) REVERT: B 677 MET cc_start: 0.8243 (mtm) cc_final: 0.7847 (mtm) REVERT: B 704 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: B 717 MET cc_start: 0.8575 (tmm) cc_final: 0.8288 (tmm) REVERT: C 144 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8660 (mm-30) REVERT: C 173 MET cc_start: 0.9189 (mtt) cc_final: 0.8941 (mtp) REVERT: C 481 TRP cc_start: 0.5648 (t60) cc_final: 0.5040 (m100) REVERT: C 704 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: D 144 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8643 (mm-30) REVERT: D 481 TRP cc_start: 0.5636 (t60) cc_final: 0.5033 (m100) REVERT: D 704 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8012 (tt0) outliers start: 45 outliers final: 36 residues processed: 227 average time/residue: 0.1329 time to fit residues: 49.5469 Evaluate side-chains 233 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 541 LEU 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 398 THR 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 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 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 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 398 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 129 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 chunk 183 optimal weight: 20.0000 chunk 147 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.0030 chunk 3 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 overall best weight: 2.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082196 restraints weight = 38828.304| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.34 r_work: 0.2970 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20680 Z= 0.156 Angle : 0.588 11.295 27844 Z= 0.292 Chirality : 0.040 0.219 3112 Planarity : 0.003 0.031 3416 Dihedral : 17.909 160.803 3140 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.97 % Allowed : 14.63 % 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: -0.15 (0.17), residues: 2372 helix: 1.12 (0.13), residues: 1548 sheet: -1.59 (0.64), residues: 64 loop : -2.61 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 716 TYR 0.011 0.001 TYR D 260 PHE 0.011 0.001 PHE A 715 TRP 0.009 0.001 TRP D 380 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00371 (20680) covalent geometry : angle 0.58850 (27844) hydrogen bonds : bond 0.03391 ( 984) hydrogen bonds : angle 3.44377 ( 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 231 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.799 Fit side-chains REVERT: A 144 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8608 (mm-30) REVERT: A 481 TRP cc_start: 0.5625 (t60) cc_final: 0.5012 (m100) REVERT: A 704 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: B 144 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8663 (mm-30) REVERT: B 173 MET cc_start: 0.9193 (mtt) cc_final: 0.8948 (mtp) REVERT: B 481 TRP cc_start: 0.5552 (t60) cc_final: 0.5043 (m100) REVERT: B 704 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: B 717 MET cc_start: 0.8639 (tmm) cc_final: 0.8402 (tmm) REVERT: C 144 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8661 (mm-30) REVERT: C 481 TRP cc_start: 0.5654 (t60) cc_final: 0.5041 (m100) REVERT: C 704 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: D 144 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8652 (mm-30) REVERT: D 481 TRP cc_start: 0.5644 (t60) cc_final: 0.5035 (m100) REVERT: D 704 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8008 (tt0) outliers start: 42 outliers final: 34 residues processed: 219 average time/residue: 0.1282 time to fit residues: 46.0356 Evaluate side-chains 227 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 541 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 158 LEU 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 398 THR 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 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 378 THR Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 579 ILE 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: 1.9990 chunk 44 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 229 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 230 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.108228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.084061 restraints weight = 38625.685| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.33 r_work: 0.3004 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20680 Z= 0.110 Angle : 0.553 11.137 27844 Z= 0.273 Chirality : 0.038 0.213 3112 Planarity : 0.003 0.031 3416 Dihedral : 17.127 160.187 3140 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.74 % Allowed : 15.01 % Favored : 83.26 % 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: 0.13 (0.18), residues: 2372 helix: 1.39 (0.13), residues: 1512 sheet: -1.54 (0.63), residues: 64 loop : -2.44 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 716 TYR 0.008 0.001 TYR B 321 PHE 0.007 0.001 PHE A 715 TRP 0.012 0.001 TRP B 739 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00255 (20680) covalent geometry : angle 0.55319 (27844) hydrogen bonds : bond 0.02977 ( 984) hydrogen bonds : angle 3.34838 ( 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 235 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.802 Fit side-chains REVERT: A 144 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8663 (mm-30) REVERT: A 450 PHE cc_start: 0.8124 (m-80) cc_final: 0.7614 (t80) REVERT: A 481 TRP cc_start: 0.5594 (t60) cc_final: 0.5024 (m100) REVERT: A 704 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: B 144 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8685 (mm-30) REVERT: B 173 MET cc_start: 0.9155 (mtt) cc_final: 0.8946 (mtp) REVERT: B 481 TRP cc_start: 0.5589 (t60) cc_final: 0.5079 (m100) REVERT: B 704 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: C 144 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8708 (mm-30) REVERT: C 481 TRP cc_start: 0.5637 (t60) cc_final: 0.5042 (m100) REVERT: C 704 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: D 144 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8681 (mm-30) REVERT: D 481 TRP cc_start: 0.5645 (t60) cc_final: 0.5044 (m100) REVERT: D 704 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8028 (tt0) outliers start: 37 outliers final: 30 residues processed: 224 average time/residue: 0.1311 time to fit residues: 48.2155 Evaluate side-chains 231 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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 378 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 541 LEU 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 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 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 398 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 117 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.085185 restraints weight = 39186.964| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.35 r_work: 0.3025 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2587 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= 0.096 Angle : 0.540 11.569 27844 Z= 0.266 Chirality : 0.037 0.197 3112 Planarity : 0.003 0.041 3416 Dihedral : 16.545 160.439 3140 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.74 % Allowed : 15.20 % Favored : 83.07 % 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: 0.28 (0.18), residues: 2372 helix: 1.51 (0.13), residues: 1512 sheet: -1.54 (0.63), residues: 64 loop : -2.38 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 716 TYR 0.007 0.001 TYR C 321 PHE 0.010 0.001 PHE B 715 TRP 0.012 0.001 TRP B 739 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00218 (20680) covalent geometry : angle 0.54024 (27844) hydrogen bonds : bond 0.02803 ( 984) hydrogen bonds : angle 3.28809 ( 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 236 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 1.161 Fit side-chains REVERT: A 144 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8611 (mm-30) REVERT: A 450 PHE cc_start: 0.8085 (m-80) cc_final: 0.7526 (t80) REVERT: A 481 TRP cc_start: 0.5538 (t60) cc_final: 0.5007 (m100) REVERT: A 704 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: B 144 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8690 (mm-30) REVERT: B 450 PHE cc_start: 0.8082 (m-80) cc_final: 0.7527 (t80) REVERT: B 481 TRP cc_start: 0.5575 (t60) cc_final: 0.5027 (m100) REVERT: B 704 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: C 144 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8650 (mm-30) REVERT: C 450 PHE cc_start: 0.8094 (m-80) cc_final: 0.7531 (t80) REVERT: C 481 TRP cc_start: 0.5673 (t60) cc_final: 0.5061 (m100) REVERT: C 704 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: D 144 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8631 (mm-30) REVERT: D 450 PHE cc_start: 0.8085 (m-80) cc_final: 0.7529 (t80) REVERT: D 481 TRP cc_start: 0.5667 (t60) cc_final: 0.5060 (m100) REVERT: D 704 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7998 (tt0) outliers start: 37 outliers final: 29 residues processed: 226 average time/residue: 0.1313 time to fit residues: 48.5744 Evaluate side-chains 227 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 A residue 635 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 158 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 398 THR Chi-restraints excluded: chain B residue 588 LEU 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 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 704 GLU 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 398 THR Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 704 GLU 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: 0.8980 chunk 90 optimal weight: 6.9990 chunk 205 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 65 optimal weight: 0.0980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083452 restraints weight = 38832.322| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.34 r_work: 0.2994 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20680 Z= 0.129 Angle : 0.573 11.782 27844 Z= 0.282 Chirality : 0.039 0.195 3112 Planarity : 0.003 0.031 3416 Dihedral : 16.645 160.727 3140 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.69 % Allowed : 15.38 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2372 helix: 1.36 (0.13), residues: 1536 sheet: -1.54 (0.63), residues: 64 loop : -2.45 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 716 TYR 0.010 0.001 TYR A 260 PHE 0.008 0.001 PHE A 715 TRP 0.010 0.001 TRP B 380 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00305 (20680) covalent geometry : angle 0.57322 (27844) hydrogen bonds : bond 0.03143 ( 984) hydrogen bonds : angle 3.36035 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4444.51 seconds wall clock time: 77 minutes 3.19 seconds (4623.19 seconds total)