Starting phenix.real_space_refine on Sun Sep 29 17:18:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mij_23853/09_2024/7mij_23853.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mij_23853/09_2024/7mij_23853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mij_23853/09_2024/7mij_23853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mij_23853/09_2024/7mij_23853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mij_23853/09_2024/7mij_23853.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mij_23853/09_2024/7mij_23853.cif" } resolution = 1.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 36 5.49 5 S 124 5.16 5 Na 2 4.78 5 C 15040 2.51 5 N 3460 2.21 5 O 4348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23010 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5202 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "B" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5202 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "C" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5202 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "D" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5202 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "A" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 626 Unusual residues: {' NA': 2, 'POV': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 312 Unusual residues: {'POV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Time building chain proxies: 13.16, per 1000 atoms: 0.57 Number of scatterers: 23010 At special positions: 0 Unit cell: (126.42, 126.42, 133.3, 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 124 16.00 P 36 15.00 Na 2 11.00 O 4348 8.00 N 3460 7.00 C 15040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 2.7 seconds 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 4 sheets defined 65.8% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.628A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.896A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.544A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.930A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.899A pdb=" N GLY A 258 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.585A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.972A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.534A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 508 removed outlier: 4.145A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.517A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.652A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.578A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 607 removed outlier: 3.578A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 685 removed outlier: 3.663A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 706 removed outlier: 3.827A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.597A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.896A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 159 Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.545A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.930A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.899A pdb=" N GLY B 258 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.586A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.972A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.533A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 508 removed outlier: 4.145A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 519 Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.516A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.654A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.577A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 607 removed outlier: 3.577A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.663A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 706 removed outlier: 3.827A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.597A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.897A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.545A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.930A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 Processing helix chain 'C' and resid 254 through 258 removed outlier: 3.899A pdb=" N GLY C 258 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.586A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.972A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.534A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 508 removed outlier: 4.146A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 519 Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.517A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.654A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.578A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 607 removed outlier: 3.578A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 685 removed outlier: 3.662A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 706 removed outlier: 3.827A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.598A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.897A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.545A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.931A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 Processing helix chain 'D' and resid 254 through 258 removed outlier: 3.898A pdb=" N GLY D 258 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.586A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.972A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.534A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 508 removed outlier: 4.145A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 519 Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.517A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.653A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.577A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 607 removed outlier: 3.578A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 685 removed outlier: 3.663A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 706 removed outlier: 3.827A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.599A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 7.096A pdb=" N LYS A 376 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP A 391 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 7.096A pdb=" N LYS B 376 " --> pdb=" O ASP B 391 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP B 391 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 7.096A pdb=" N LYS C 376 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP C 391 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 7.097A pdb=" N LYS D 376 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP D 391 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1108 hydrogen bonds defined for protein. 3216 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: 6.78 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3428 1.31 - 1.44: 5981 1.44 - 1.56: 13410 1.56 - 1.69: 77 1.69 - 1.82: 204 Bond restraints: 23100 Sorted by residual: bond pdb=" C21 POV B 909 " pdb=" O21 POV B 909 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C21 POV C 909 " pdb=" O21 POV C 909 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C21 POV A 911 " pdb=" O21 POV A 911 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C21 POV B 901 " pdb=" O21 POV B 901 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C21 POV A 905 " pdb=" O21 POV A 905 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 2.00e+01 ... (remaining 23095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 29726 2.80 - 5.60: 770 5.60 - 8.41: 232 8.41 - 11.21: 107 11.21 - 14.01: 77 Bond angle restraints: 30912 Sorted by residual: angle pdb=" C LYS D 614 " pdb=" N ASP D 615 " pdb=" CA ASP D 615 " ideal model delta sigma weight residual 120.82 129.64 -8.82 1.50e+00 4.44e-01 3.46e+01 angle pdb=" C LYS A 614 " pdb=" N ASP A 615 " pdb=" CA ASP A 615 " ideal model delta sigma weight residual 120.82 129.61 -8.79 1.50e+00 4.44e-01 3.44e+01 angle pdb=" C LYS C 614 " pdb=" N ASP C 615 " pdb=" CA ASP C 615 " ideal model delta sigma weight residual 120.82 129.59 -8.77 1.50e+00 4.44e-01 3.42e+01 angle pdb=" C LYS B 614 " pdb=" N ASP B 615 " pdb=" CA ASP B 615 " ideal model delta sigma weight residual 120.82 129.55 -8.73 1.50e+00 4.44e-01 3.39e+01 angle pdb=" N GLN A 313 " pdb=" CA GLN A 313 " pdb=" CB GLN A 313 " ideal model delta sigma weight residual 110.80 103.81 6.99 1.49e+00 4.50e-01 2.20e+01 ... (remaining 30907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 13470 35.18 - 70.36: 654 70.36 - 105.53: 96 105.53 - 140.71: 36 140.71 - 175.89: 12 Dihedral angle restraints: 14268 sinusoidal: 6724 harmonic: 7544 Sorted by residual: dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual 93.00 173.79 -80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual 93.00 173.78 -80.78 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual 93.00 173.78 -80.78 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 14265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2604 0.054 - 0.109: 588 0.109 - 0.163: 94 0.163 - 0.217: 31 0.217 - 0.272: 7 Chirality restraints: 3324 Sorted by residual: chirality pdb=" CA ASN A 314 " pdb=" N ASN A 314 " pdb=" C ASN A 314 " pdb=" CB ASN A 314 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ASN D 314 " pdb=" N ASN D 314 " pdb=" C ASN D 314 " pdb=" CB ASN D 314 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASN C 314 " pdb=" N ASN C 314 " pdb=" C ASN C 314 " pdb=" CB ASN C 314 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 3321 not shown) Planarity restraints: 3704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 311 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C LYS B 311 " -0.058 2.00e-02 2.50e+03 pdb=" O LYS B 311 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 312 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 509 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.91e+00 pdb=" N PRO B 510 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 510 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 510 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 509 " -0.052 5.00e-02 4.00e+02 7.85e-02 9.87e+00 pdb=" N PRO D 510 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 510 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 510 " -0.043 5.00e-02 4.00e+02 ... (remaining 3701 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6551 2.84 - 3.35: 19720 3.35 - 3.87: 35478 3.87 - 4.38: 43603 4.38 - 4.90: 72412 Nonbonded interactions: 177764 Sorted by model distance: nonbonded pdb=" O ALA A 206 " pdb=" O HOH A1001 " model vdw 2.320 3.040 nonbonded pdb=" O GLN A 255 " pdb=" O HOH A1002 " model vdw 2.327 3.040 nonbonded pdb=" O GLN C 255 " pdb=" O HOH C1001 " model vdw 2.339 3.040 nonbonded pdb=" O GLN D 255 " pdb=" O HOH D1001 " model vdw 2.342 3.040 nonbonded pdb=" O THR A 393 " pdb=" O HOH A1003 " model vdw 2.343 3.040 ... (remaining 177759 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 118 through 756 or resid 901 through 906)) selection = (chain 'B' and (resid 118 through 756 or resid 901 through 906)) selection = (chain 'C' and (resid 118 through 756 or resid 901 through 906)) 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=0.45 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: 6.950 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: 0.000 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 46.340 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.080 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 : 0.010 0.090 23100 Z= 0.571 Angle : 1.379 14.011 30912 Z= 0.610 Chirality : 0.049 0.272 3324 Planarity : 0.006 0.079 3704 Dihedral : 20.526 175.890 9360 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.18 % Allowed : 4.96 % Favored : 94.87 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.12), residues: 2548 helix: -2.98 (0.09), residues: 1540 sheet: 0.69 (0.53), residues: 88 loop : -1.97 (0.16), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 692 HIS 0.007 0.002 HIS D 301 PHE 0.041 0.003 PHE A 526 TYR 0.020 0.003 TYR A 540 ARG 0.007 0.001 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 428 time to evaluate : 2.359 Fit side-chains REVERT: A 479 MET cc_start: 0.1459 (ptp) cc_final: 0.1216 (tmm) REVERT: A 497 ILE cc_start: 0.7532 (mt) cc_final: 0.6777 (mp) REVERT: A 501 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6339 (mp0) REVERT: B 497 ILE cc_start: 0.7663 (mt) cc_final: 0.7146 (mp) REVERT: B 501 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6280 (mp0) REVERT: B 578 MET cc_start: 0.8127 (tpp) cc_final: 0.7827 (tpp) REVERT: C 497 ILE cc_start: 0.7666 (mt) cc_final: 0.6923 (mp) REVERT: C 501 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6314 (mp0) REVERT: C 578 MET cc_start: 0.8143 (tpp) cc_final: 0.7919 (tpp) REVERT: D 497 ILE cc_start: 0.7678 (mt) cc_final: 0.7162 (mp) REVERT: D 501 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6308 (mp0) REVERT: D 578 MET cc_start: 0.8137 (tpp) cc_final: 0.7902 (tpp) outliers start: 4 outliers final: 0 residues processed: 431 average time/residue: 1.4168 time to fit residues: 691.0484 Evaluate side-chains 265 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 228 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 178 ASN A 220 ASN A 227 GLN A 274 GLN A 426 HIS A 477 HIS A 523 HIS A 643 ASN A 647 ASN A 750 ASN B 220 ASN B 227 GLN B 274 GLN B 426 HIS B 477 HIS B 523 HIS B 643 ASN B 647 ASN C 220 ASN C 227 GLN C 274 GLN C 426 HIS C 477 HIS C 523 HIS C 643 ASN C 647 ASN C 750 ASN D 220 ASN D 227 GLN D 274 GLN D 426 HIS D 477 HIS D 523 HIS D 643 ASN D 647 ASN D 750 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23100 Z= 0.174 Angle : 0.593 8.143 30912 Z= 0.321 Chirality : 0.040 0.138 3324 Planarity : 0.005 0.056 3704 Dihedral : 24.387 151.123 4328 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.37 % Allowed : 6.84 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 2548 helix: 0.15 (0.12), residues: 1580 sheet: 0.85 (0.52), residues: 88 loop : -1.60 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 692 HIS 0.004 0.001 HIS C 523 PHE 0.020 0.002 PHE D 316 TYR 0.024 0.002 TYR D 540 ARG 0.004 0.001 ARG A 714 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 293 time to evaluate : 2.387 Fit side-chains REVERT: A 327 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6485 (tpp-160) REVERT: A 578 MET cc_start: 0.8074 (tpp) cc_final: 0.7828 (tpp) REVERT: A 682 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: B 121 LYS cc_start: 0.6785 (mptm) cc_final: 0.6495 (mptt) REVERT: B 327 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.5779 (mmm-85) REVERT: B 495 THR cc_start: 0.7366 (m) cc_final: 0.7159 (p) REVERT: B 645 GLN cc_start: 0.6152 (OUTLIER) cc_final: 0.5615 (mp10) REVERT: B 682 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7226 (tp30) REVERT: C 121 LYS cc_start: 0.6779 (mptm) cc_final: 0.6494 (mptt) REVERT: C 327 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.5697 (mmm-85) REVERT: C 645 GLN cc_start: 0.6141 (OUTLIER) cc_final: 0.5652 (mp10) REVERT: C 682 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: D 121 LYS cc_start: 0.6758 (mptm) cc_final: 0.6475 (mptt) REVERT: D 327 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.5654 (mmm-85) REVERT: D 645 GLN cc_start: 0.6146 (OUTLIER) cc_final: 0.5657 (mp10) REVERT: D 682 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7209 (tp30) outliers start: 54 outliers final: 4 residues processed: 319 average time/residue: 1.5575 time to fit residues: 558.9041 Evaluate side-chains 272 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 257 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 155 optimal weight: 0.2980 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 247 optimal weight: 0.7980 chunk 204 optimal weight: 0.6980 chunk 227 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 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 580 GLN A 750 ASN B 580 GLN C 580 GLN C 750 ASN D 580 GLN D 750 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23100 Z= 0.160 Angle : 0.552 7.044 30912 Z= 0.296 Chirality : 0.039 0.138 3324 Planarity : 0.004 0.046 3704 Dihedral : 22.866 152.886 4328 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.68 % Allowed : 7.76 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 2548 helix: 1.16 (0.13), residues: 1588 sheet: 0.86 (0.50), residues: 88 loop : -1.49 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 692 HIS 0.005 0.001 HIS A 426 PHE 0.020 0.002 PHE C 316 TYR 0.024 0.002 TYR B 540 ARG 0.006 0.001 ARG B 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 278 time to evaluate : 2.375 Fit side-chains REVERT: A 327 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6513 (tpp-160) REVERT: A 434 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7840 (mmtt) REVERT: A 479 MET cc_start: 0.0991 (OUTLIER) cc_final: 0.0664 (tmm) REVERT: B 121 LYS cc_start: 0.6758 (mptm) cc_final: 0.6469 (mptt) REVERT: B 327 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.5767 (mmm-85) REVERT: B 495 THR cc_start: 0.7387 (m) cc_final: 0.7181 (p) REVERT: B 645 GLN cc_start: 0.6155 (OUTLIER) cc_final: 0.5678 (mp10) REVERT: B 682 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7169 (tp30) REVERT: B 750 ASN cc_start: 0.7730 (m110) cc_final: 0.7374 (t0) REVERT: C 121 LYS cc_start: 0.6734 (mptm) cc_final: 0.6455 (mptt) REVERT: C 327 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.5766 (mmm-85) REVERT: C 645 GLN cc_start: 0.6139 (OUTLIER) cc_final: 0.5664 (mp10) REVERT: C 682 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: D 121 LYS cc_start: 0.6738 (mptm) cc_final: 0.6485 (mptt) REVERT: D 327 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.5769 (mmm-85) REVERT: D 434 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7778 (mmtt) REVERT: D 645 GLN cc_start: 0.6139 (OUTLIER) cc_final: 0.5716 (mp10) REVERT: D 682 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7148 (tp30) outliers start: 61 outliers final: 15 residues processed: 312 average time/residue: 1.5336 time to fit residues: 538.9008 Evaluate side-chains 268 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 240 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 717 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 580 GLN C 178 ASN C 580 GLN D 580 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23100 Z= 0.231 Angle : 0.659 7.304 30912 Z= 0.351 Chirality : 0.043 0.156 3324 Planarity : 0.005 0.051 3704 Dihedral : 22.788 157.547 4328 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.46 % Allowed : 8.42 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2548 helix: 1.06 (0.12), residues: 1604 sheet: 0.91 (0.50), residues: 88 loop : -1.54 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 493 HIS 0.008 0.002 HIS B 426 PHE 0.029 0.002 PHE D 449 TYR 0.029 0.003 TYR B 540 ARG 0.007 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 250 time to evaluate : 2.442 Fit side-chains REVERT: A 158 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6654 (tt) REVERT: A 253 LYS cc_start: 0.6615 (mmmt) cc_final: 0.6312 (mmmt) REVERT: A 327 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.5868 (mmm-85) REVERT: A 682 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7242 (tp30) REVERT: B 158 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6643 (tt) REVERT: B 327 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.5852 (mmm-85) REVERT: B 479 MET cc_start: 0.1213 (OUTLIER) cc_final: 0.0764 (tmm) REVERT: B 645 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.5752 (mp10) REVERT: B 682 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: B 750 ASN cc_start: 0.7671 (m110) cc_final: 0.7357 (t0) REVERT: C 158 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6588 (tt) REVERT: C 327 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.5863 (mmm-85) REVERT: C 645 GLN cc_start: 0.6239 (OUTLIER) cc_final: 0.5739 (mp10) REVERT: C 682 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: C 750 ASN cc_start: 0.7657 (m110) cc_final: 0.7372 (t0) REVERT: D 158 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6594 (tt) REVERT: D 327 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.5851 (mmm-85) REVERT: D 371 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6303 (ttp-170) REVERT: D 645 GLN cc_start: 0.6258 (OUTLIER) cc_final: 0.5752 (mp10) REVERT: D 682 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7257 (tp30) REVERT: D 750 ASN cc_start: 0.7646 (m110) cc_final: 0.7365 (t0) outliers start: 56 outliers final: 13 residues processed: 281 average time/residue: 1.5757 time to fit residues: 497.3454 Evaluate side-chains 275 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23100 Z= 0.248 Angle : 0.675 7.147 30912 Z= 0.360 Chirality : 0.044 0.148 3324 Planarity : 0.005 0.057 3704 Dihedral : 22.627 157.339 4328 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.50 % Allowed : 9.30 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2548 helix: 0.95 (0.12), residues: 1628 sheet: 0.84 (0.51), residues: 88 loop : -1.67 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 493 HIS 0.008 0.002 HIS D 426 PHE 0.032 0.002 PHE B 449 TYR 0.033 0.003 TYR A 540 ARG 0.007 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 269 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6657 (tt) REVERT: A 253 LYS cc_start: 0.6661 (mmmt) cc_final: 0.6357 (mmmt) REVERT: A 327 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.5866 (mmm-85) REVERT: A 434 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7951 (mmtt) REVERT: A 682 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7251 (tp30) REVERT: B 158 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6575 (tt) REVERT: B 327 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.5863 (mmm-85) REVERT: B 645 GLN cc_start: 0.6308 (OUTLIER) cc_final: 0.5841 (mp10) REVERT: B 682 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: B 750 ASN cc_start: 0.7671 (m110) cc_final: 0.7367 (t0) REVERT: C 158 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6483 (tt) REVERT: C 327 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.5874 (mmm-85) REVERT: C 645 GLN cc_start: 0.6321 (OUTLIER) cc_final: 0.5851 (mp10) REVERT: C 682 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7279 (tp30) REVERT: C 750 ASN cc_start: 0.7657 (m110) cc_final: 0.7380 (t0) REVERT: D 158 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6546 (tt) REVERT: D 327 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.5869 (mmm-85) REVERT: D 371 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6325 (ttp-170) REVERT: D 434 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7884 (mmtt) REVERT: D 645 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.5845 (mp10) REVERT: D 682 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7246 (tp30) REVERT: D 750 ASN cc_start: 0.7643 (m110) cc_final: 0.7362 (t0) outliers start: 57 outliers final: 20 residues processed: 300 average time/residue: 1.5431 time to fit residues: 520.4922 Evaluate side-chains 287 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 249 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 687 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.9990 chunk 219 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 580 GLN C 580 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23100 Z= 0.146 Angle : 0.528 8.067 30912 Z= 0.283 Chirality : 0.039 0.128 3324 Planarity : 0.004 0.049 3704 Dihedral : 21.296 152.991 4328 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.28 % Allowed : 9.87 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.16), residues: 2548 helix: 1.57 (0.13), residues: 1636 sheet: 0.91 (0.50), residues: 88 loop : -1.63 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 493 HIS 0.004 0.001 HIS C 426 PHE 0.029 0.001 PHE B 449 TYR 0.025 0.002 TYR A 540 ARG 0.007 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 267 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LYS cc_start: 0.6604 (mmmt) cc_final: 0.6378 (mmmt) REVERT: A 327 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.5927 (mmm-85) REVERT: A 682 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7137 (tp30) REVERT: A 687 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6884 (pm20) REVERT: B 158 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6458 (tt) REVERT: B 327 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.5777 (mmm-85) REVERT: B 337 ARG cc_start: 0.7793 (mtt-85) cc_final: 0.7585 (mtt180) REVERT: B 682 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7152 (tp30) REVERT: B 687 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: B 750 ASN cc_start: 0.7642 (m110) cc_final: 0.7340 (t0) REVERT: C 158 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6453 (tt) REVERT: C 314 ASN cc_start: 0.7151 (OUTLIER) cc_final: 0.6897 (m-40) REVERT: C 327 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.5789 (mmm-85) REVERT: C 337 ARG cc_start: 0.7789 (mtt-85) cc_final: 0.7588 (mtt180) REVERT: C 682 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7189 (tp30) REVERT: C 750 ASN cc_start: 0.7649 (m110) cc_final: 0.7361 (t0) REVERT: D 158 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6474 (tt) REVERT: D 314 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6878 (m-40) REVERT: D 327 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.5778 (mmm-85) REVERT: D 337 ARG cc_start: 0.7789 (mtt-85) cc_final: 0.7584 (mtt180) REVERT: D 682 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7152 (tp30) REVERT: D 750 ASN cc_start: 0.7650 (m110) cc_final: 0.7360 (t0) outliers start: 52 outliers final: 11 residues processed: 292 average time/residue: 1.5771 time to fit residues: 518.0655 Evaluate side-chains 266 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 240 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 138 optimal weight: 0.0770 chunk 178 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 overall best weight: 1.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23100 Z= 0.232 Angle : 0.652 7.938 30912 Z= 0.347 Chirality : 0.043 0.188 3324 Planarity : 0.005 0.052 3704 Dihedral : 21.549 154.791 4328 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.41 % Allowed : 10.66 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.16), residues: 2548 helix: 1.28 (0.12), residues: 1628 sheet: 0.85 (0.52), residues: 88 loop : -1.64 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 493 HIS 0.006 0.002 HIS D 426 PHE 0.024 0.002 PHE D 316 TYR 0.030 0.003 TYR A 540 ARG 0.007 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 255 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6647 (tt) REVERT: A 253 LYS cc_start: 0.6662 (mmmt) cc_final: 0.6357 (mmmt) REVERT: A 327 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.5862 (mmm-85) REVERT: A 682 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7254 (tp30) REVERT: B 158 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6503 (tt) REVERT: B 327 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5860 (mmm-85) REVERT: B 645 GLN cc_start: 0.6174 (OUTLIER) cc_final: 0.5696 (mp10) REVERT: B 682 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7242 (tp30) REVERT: B 750 ASN cc_start: 0.7662 (m110) cc_final: 0.7352 (t0) REVERT: C 158 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6462 (tt) REVERT: C 327 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.5866 (mmm-85) REVERT: C 645 GLN cc_start: 0.6180 (OUTLIER) cc_final: 0.5701 (mp10) REVERT: C 682 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7265 (tp30) REVERT: C 750 ASN cc_start: 0.7673 (m110) cc_final: 0.7392 (t0) REVERT: D 158 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6450 (tt) REVERT: D 327 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.5860 (mmm-85) REVERT: D 645 GLN cc_start: 0.6175 (OUTLIER) cc_final: 0.5698 (mp10) REVERT: D 682 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7231 (tp30) REVERT: D 750 ASN cc_start: 0.7657 (m110) cc_final: 0.7370 (t0) outliers start: 55 outliers final: 21 residues processed: 289 average time/residue: 1.4992 time to fit residues: 488.5567 Evaluate side-chains 288 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 252 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 22 optimal weight: 0.0570 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 580 GLN D 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23100 Z= 0.144 Angle : 0.523 7.833 30912 Z= 0.279 Chirality : 0.039 0.128 3324 Planarity : 0.004 0.047 3704 Dihedral : 20.534 150.941 4328 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.19 % Allowed : 10.66 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.16), residues: 2548 helix: 1.71 (0.13), residues: 1640 sheet: 0.76 (0.52), residues: 88 loop : -1.62 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 493 HIS 0.004 0.001 HIS C 301 PHE 0.028 0.001 PHE D 449 TYR 0.024 0.002 TYR A 540 ARG 0.006 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 275 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LYS cc_start: 0.6605 (mmmt) cc_final: 0.6339 (mmmt) REVERT: A 327 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.5810 (mmm-85) REVERT: A 682 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7123 (tp30) REVERT: B 158 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6534 (tt) REVERT: B 327 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.5821 (mmm-85) REVERT: B 682 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7145 (tp30) REVERT: B 728 PHE cc_start: 0.8177 (m-80) cc_final: 0.7959 (m-80) REVERT: B 750 ASN cc_start: 0.7667 (m110) cc_final: 0.7355 (t0) REVERT: C 158 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6486 (tt) REVERT: C 327 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.5833 (mmm-85) REVERT: C 682 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7171 (tp30) REVERT: C 750 ASN cc_start: 0.7682 (m110) cc_final: 0.7385 (t0) REVERT: D 158 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6496 (tt) REVERT: D 327 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.5819 (mmm-85) REVERT: D 682 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7132 (tp30) REVERT: D 750 ASN cc_start: 0.7665 (m110) cc_final: 0.7377 (t0) outliers start: 50 outliers final: 15 residues processed: 305 average time/residue: 1.5548 time to fit residues: 533.3930 Evaluate side-chains 278 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 252 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 225 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 580 GLN A 647 ASN B 580 GLN B 647 ASN C 580 GLN C 647 ASN D 580 GLN D 647 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23100 Z= 0.213 Angle : 0.633 8.382 30912 Z= 0.336 Chirality : 0.042 0.139 3324 Planarity : 0.004 0.051 3704 Dihedral : 20.802 152.469 4328 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.02 % Allowed : 11.36 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2548 helix: 1.55 (0.12), residues: 1604 sheet: 0.58 (0.52), residues: 88 loop : -1.56 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 493 HIS 0.006 0.002 HIS B 426 PHE 0.023 0.002 PHE D 316 TYR 0.028 0.002 TYR A 540 ARG 0.008 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 257 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6650 (tt) REVERT: A 253 LYS cc_start: 0.6637 (mmmt) cc_final: 0.6339 (mmmt) REVERT: A 327 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.5862 (mmm-85) REVERT: A 682 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7214 (tp30) REVERT: B 158 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6493 (tt) REVERT: B 327 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.5865 (mmm-85) REVERT: B 645 GLN cc_start: 0.6088 (OUTLIER) cc_final: 0.5719 (mp10) REVERT: B 682 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: B 728 PHE cc_start: 0.8186 (m-80) cc_final: 0.7950 (m-80) REVERT: B 750 ASN cc_start: 0.7672 (m110) cc_final: 0.7359 (t0) REVERT: C 158 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6435 (tt) REVERT: C 327 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.5887 (mmm-85) REVERT: C 645 GLN cc_start: 0.6178 (OUTLIER) cc_final: 0.5775 (mp10) REVERT: C 682 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: C 750 ASN cc_start: 0.7668 (m110) cc_final: 0.7390 (t0) REVERT: D 158 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6475 (tt) REVERT: D 327 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.5880 (mmm-85) REVERT: D 645 GLN cc_start: 0.6173 (OUTLIER) cc_final: 0.5763 (mp10) REVERT: D 682 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7219 (tp30) REVERT: D 750 ASN cc_start: 0.7669 (m110) cc_final: 0.7382 (t0) outliers start: 46 outliers final: 14 residues processed: 287 average time/residue: 1.6091 time to fit residues: 517.8607 Evaluate side-chains 279 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 250 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 0.0470 chunk 158 optimal weight: 0.6980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 647 ASN C 580 GLN C 647 ASN D 580 GLN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23100 Z= 0.157 Angle : 0.554 8.351 30912 Z= 0.294 Chirality : 0.039 0.136 3324 Planarity : 0.004 0.047 3704 Dihedral : 20.331 150.289 4328 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.49 % Allowed : 11.71 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.16), residues: 2548 helix: 1.78 (0.13), residues: 1616 sheet: 0.60 (0.52), residues: 88 loop : -1.53 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 493 HIS 0.004 0.001 HIS C 301 PHE 0.031 0.001 PHE D 449 TYR 0.025 0.002 TYR A 540 ARG 0.007 0.000 ARG A 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 260 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6669 (tt) REVERT: A 253 LYS cc_start: 0.6595 (mmmt) cc_final: 0.6317 (mmmt) REVERT: A 327 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.5854 (mmm-85) REVERT: A 682 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7139 (tp30) REVERT: B 158 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6501 (tt) REVERT: B 327 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.5922 (mmm-85) REVERT: B 682 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7157 (tp30) REVERT: B 728 PHE cc_start: 0.8177 (m-80) cc_final: 0.7968 (m-80) REVERT: B 750 ASN cc_start: 0.7680 (m110) cc_final: 0.7366 (t0) REVERT: C 158 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6478 (tt) REVERT: C 327 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.5934 (mmm-85) REVERT: C 682 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7199 (tp30) REVERT: C 750 ASN cc_start: 0.7682 (m110) cc_final: 0.7386 (t0) REVERT: D 158 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6463 (tt) REVERT: D 327 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.5926 (mmm-85) REVERT: D 682 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7166 (tp30) REVERT: D 750 ASN cc_start: 0.7666 (m110) cc_final: 0.7371 (t0) outliers start: 34 outliers final: 15 residues processed: 284 average time/residue: 1.6167 time to fit residues: 515.2712 Evaluate side-chains 285 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 258 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 GLN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.192911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.159180 restraints weight = 16528.586| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 0.86 r_work: 0.3586 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23100 Z= 0.207 Angle : 0.623 8.225 30912 Z= 0.330 Chirality : 0.041 0.139 3324 Planarity : 0.004 0.050 3704 Dihedral : 20.554 150.862 4328 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.36 % Allowed : 11.97 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.16), residues: 2548 helix: 1.61 (0.12), residues: 1612 sheet: 0.62 (0.52), residues: 88 loop : -1.59 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 493 HIS 0.006 0.002 HIS A 426 PHE 0.033 0.002 PHE B 449 TYR 0.028 0.002 TYR A 540 ARG 0.004 0.001 ARG C 729 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8938.90 seconds wall clock time: 157 minutes 31.04 seconds (9451.04 seconds total)