Starting phenix.real_space_refine on Fri Nov 15 12:42:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3a_35147/11_2024/8i3a_35147.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3a_35147/11_2024/8i3a_35147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3a_35147/11_2024/8i3a_35147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3a_35147/11_2024/8i3a_35147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3a_35147/11_2024/8i3a_35147.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3a_35147/11_2024/8i3a_35147.cif" } resolution = 3.04 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= 0.001 sd= 0.140 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 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5730 2.51 5 N 1476 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8830 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4383 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4383 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.12, per 1000 atoms: 0.69 Number of scatterers: 8830 At special positions: 0 Unit cell: (75.53, 92.13, 119.52, 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 54 16.00 P 6 15.00 Mg 2 11.99 O 1562 8.00 N 1476 7.00 C 5730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 54.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.561A pdb=" N VAL A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.834A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 255 removed outlier: 3.791A pdb=" N LEU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.674A pdb=" N GLN A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 336 through 349 Processing helix chain 'A' and resid 349 through 358 removed outlier: 3.668A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 3.741A pdb=" N ALA A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.529A pdb=" N ALA A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 removed outlier: 3.600A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.504A pdb=" N ASN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.773A pdb=" N ARG A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 485 removed outlier: 3.677A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 508 removed outlier: 4.061A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 540 removed outlier: 3.562A pdb=" N PHE A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 561 removed outlier: 3.909A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.999A pdb=" N VAL A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 4.377A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 658 removed outlier: 3.884A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 190 removed outlier: 3.561A pdb=" N VAL B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.834A pdb=" N ARG B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 255 removed outlier: 3.791A pdb=" N LEU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.675A pdb=" N GLN B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 336 through 349 Processing helix chain 'B' and resid 349 through 358 removed outlier: 3.667A pdb=" N CYS B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 removed outlier: 3.741A pdb=" N ALA B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP B 386 " --> pdb=" O CYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.529A pdb=" N ALA B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 455 removed outlier: 3.600A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.503A pdb=" N ASN B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 473 removed outlier: 3.774A pdb=" N ARG B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 485 removed outlier: 3.678A pdb=" N ALA B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 508 removed outlier: 4.061A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 540 removed outlier: 3.562A pdb=" N PHE B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 removed outlier: 3.909A pdb=" N THR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 574 removed outlier: 3.999A pdb=" N VAL B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 4.377A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 658 removed outlier: 3.884A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 91 removed outlier: 6.665A pdb=" N ARG A 81 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LYS A 50 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 83 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ARG A 48 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER A 85 " --> pdb=" O CYS A 46 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS A 46 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL A 87 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.349A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU A 95 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR A 262 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE A 96 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU A 279 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 98 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 281 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 100 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER A 282 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N CYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 91 removed outlier: 6.664A pdb=" N ARG B 81 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LYS B 50 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 83 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ARG B 48 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER B 85 " --> pdb=" O CYS B 46 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS B 46 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL B 87 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.348A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU B 95 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR B 262 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET B 97 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE B 96 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU B 279 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 98 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU B 281 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 100 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 288 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER B 282 " --> pdb=" O CYS B 286 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N CYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2366 1.33 - 1.45: 1730 1.45 - 1.57: 4826 1.57 - 1.70: 8 1.70 - 1.82: 88 Bond restraints: 9018 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " ideal model delta sigma weight residual 1.374 1.301 0.073 1.00e-02 1.00e+04 5.37e+01 bond pdb=" C4 ATP A 703 " pdb=" N9 ATP A 703 " ideal model delta sigma weight residual 1.374 1.301 0.073 1.00e-02 1.00e+04 5.27e+01 bond pdb=" C5 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.387 1.318 0.069 1.00e-02 1.00e+04 4.73e+01 bond pdb=" C5 ATP A 703 " pdb=" N7 ATP A 703 " ideal model delta sigma weight residual 1.387 1.319 0.068 1.00e-02 1.00e+04 4.68e+01 bond pdb=" C4' ATP A 701 " pdb=" O4' ATP A 701 " ideal model delta sigma weight residual 1.444 1.383 0.061 1.10e-02 8.26e+03 3.12e+01 ... (remaining 9013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 12086 3.54 - 7.08: 121 7.08 - 10.62: 23 10.62 - 14.15: 4 14.15 - 17.69: 4 Bond angle restraints: 12238 Sorted by residual: angle pdb=" PB ATP A 703 " pdb=" O3B ATP A 703 " pdb=" PG ATP A 703 " ideal model delta sigma weight residual 139.87 129.18 10.69 1.00e+00 1.00e+00 1.14e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 129.21 10.66 1.00e+00 1.00e+00 1.14e+02 angle pdb=" N3 ATP A 701 " pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " ideal model delta sigma weight residual 127.04 135.85 -8.81 1.15e+00 7.59e-01 5.89e+01 angle pdb=" N3 ATP A 703 " pdb=" C4 ATP A 703 " pdb=" N9 ATP A 703 " ideal model delta sigma weight residual 127.04 135.85 -8.81 1.15e+00 7.59e-01 5.89e+01 angle pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " ideal model delta sigma weight residual 101.57 113.31 -11.74 1.54e+00 4.24e-01 5.84e+01 ... (remaining 12233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4806 17.35 - 34.70: 443 34.70 - 52.05: 57 52.05 - 69.40: 24 69.40 - 86.75: 8 Dihedral angle restraints: 5338 sinusoidal: 2112 harmonic: 3226 Sorted by residual: dihedral pdb=" CA ALA B 297 " pdb=" C ALA B 297 " pdb=" N TYR B 298 " pdb=" CA TYR B 298 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ALA A 297 " pdb=" C ALA A 297 " pdb=" N TYR A 298 " pdb=" CA TYR A 298 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA LEU B 169 " pdb=" C LEU B 169 " pdb=" N PRO B 170 " pdb=" CA PRO B 170 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 5335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1159 0.062 - 0.125: 240 0.125 - 0.187: 50 0.187 - 0.250: 2 0.250 - 0.312: 3 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CB VAL B 566 " pdb=" CA VAL B 566 " pdb=" CG1 VAL B 566 " pdb=" CG2 VAL B 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA ASN B 567 " pdb=" N ASN B 567 " pdb=" C ASN B 567 " pdb=" CB ASN B 567 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB VAL A 566 " pdb=" CA VAL A 566 " pdb=" CG1 VAL A 566 " pdb=" CG2 VAL A 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1451 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 223 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C ILE B 223 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE B 223 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 224 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 223 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C ILE A 223 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 223 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN A 224 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 101 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.74e+00 pdb=" N PRO B 102 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.030 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 33 2.60 - 3.17: 6695 3.17 - 3.75: 13047 3.75 - 4.32: 19569 4.32 - 4.90: 32447 Nonbonded interactions: 71791 Sorted by model distance: nonbonded pdb=" O2' ATP A 701 " pdb=" O3' ATP A 701 " model vdw 2.023 2.432 nonbonded pdb=" O2' ATP A 703 " pdb=" O3' ATP A 703 " model vdw 2.024 2.432 nonbonded pdb=" OH TYR B 152 " pdb=" OE1 GLU B 462 " model vdw 2.356 3.040 nonbonded pdb=" OH TYR A 152 " pdb=" OE1 GLU A 462 " model vdw 2.357 3.040 nonbonded pdb=" OG SER B 108 " pdb="MG MG B 701 " model vdw 2.377 2.170 ... (remaining 71786 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 32 through 662) selection = (chain 'B' and resid 32 through 662) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.440 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.008 0.096 9018 Z= 0.493 Angle : 1.044 17.692 12238 Z= 0.608 Chirality : 0.056 0.312 1454 Planarity : 0.006 0.054 1488 Dihedral : 14.216 86.745 3262 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.61 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -4.99 (0.17), residues: 1104 helix: -3.22 (0.13), residues: 634 sheet: -1.97 (0.44), residues: 94 loop : -3.47 (0.24), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 447 HIS 0.006 0.001 HIS B 219 PHE 0.022 0.002 PHE B 499 TYR 0.018 0.002 TYR B 594 ARG 0.004 0.000 ARG B 587 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.003 Fit side-chains REVERT: A 141 ARG cc_start: 0.7547 (mtm180) cc_final: 0.6813 (mmm160) REVERT: A 212 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7705 (ttp80) REVERT: A 285 LYS cc_start: 0.8043 (mttp) cc_final: 0.7724 (mtpt) REVERT: A 462 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 568 LYS cc_start: 0.7914 (tptp) cc_final: 0.7321 (mtpt) REVERT: B 141 ARG cc_start: 0.7573 (mtm180) cc_final: 0.6874 (mmm160) REVERT: B 212 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7720 (ttp80) REVERT: B 274 MET cc_start: 0.8779 (mtt) cc_final: 0.8527 (mtp) REVERT: B 285 LYS cc_start: 0.8018 (mttp) cc_final: 0.7706 (mtpt) REVERT: B 402 ARG cc_start: 0.7459 (ttm170) cc_final: 0.7206 (ttm170) REVERT: B 462 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7360 (mm-30) REVERT: B 568 LYS cc_start: 0.8535 (mttt) cc_final: 0.8283 (mtpt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.3123 time to fit residues: 56.0307 Evaluate side-chains 116 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 254 HIS A 265 HIS A 321 ASN A 352 GLN B 112 ASN B 254 HIS B 265 HIS B 321 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9018 Z= 0.179 Angle : 0.538 6.427 12238 Z= 0.278 Chirality : 0.041 0.144 1454 Planarity : 0.004 0.039 1488 Dihedral : 8.583 73.711 1282 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.89 % Favored : 93.93 % Rotamer: Outliers : 0.73 % Allowed : 6.35 % Favored : 92.92 % 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: -2.97 (0.22), residues: 1104 helix: -1.29 (0.18), residues: 626 sheet: -1.94 (0.46), residues: 82 loop : -2.95 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 447 HIS 0.005 0.001 HIS B 434 PHE 0.013 0.001 PHE B 42 TYR 0.011 0.001 TYR B 594 ARG 0.001 0.000 ARG A 431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.949 Fit side-chains REVERT: A 133 LYS cc_start: 0.8440 (ptmm) cc_final: 0.8202 (ptmm) REVERT: A 141 ARG cc_start: 0.7505 (mtm180) cc_final: 0.6803 (mmm160) REVERT: A 193 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8322 (mmmt) REVERT: A 429 ASP cc_start: 0.7808 (t70) cc_final: 0.7427 (t70) REVERT: A 462 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7259 (mm-30) REVERT: A 568 LYS cc_start: 0.8010 (tptp) cc_final: 0.7478 (mtmt) REVERT: B 141 ARG cc_start: 0.7561 (mtm180) cc_final: 0.6894 (mmm160) REVERT: B 285 LYS cc_start: 0.7923 (mttp) cc_final: 0.7625 (mtpt) REVERT: B 402 ARG cc_start: 0.7456 (ttm170) cc_final: 0.7128 (ttm170) REVERT: B 429 ASP cc_start: 0.7836 (t70) cc_final: 0.7477 (t70) REVERT: B 661 LYS cc_start: 0.7392 (mttt) cc_final: 0.7134 (mttm) outliers start: 7 outliers final: 6 residues processed: 129 average time/residue: 0.3132 time to fit residues: 51.3448 Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 434 HIS B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9018 Z= 0.414 Angle : 0.642 6.548 12238 Z= 0.324 Chirality : 0.046 0.178 1454 Planarity : 0.004 0.038 1488 Dihedral : 9.190 87.320 1282 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.88 % Favored : 92.93 % Rotamer: Outliers : 1.67 % Allowed : 7.50 % Favored : 90.83 % 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: -2.57 (0.23), residues: 1104 helix: -0.97 (0.19), residues: 642 sheet: -1.72 (0.49), residues: 82 loop : -2.85 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 447 HIS 0.006 0.001 HIS A 434 PHE 0.017 0.002 PHE A 499 TYR 0.019 0.002 TYR B 594 ARG 0.003 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.089 Fit side-chains REVERT: A 133 LYS cc_start: 0.8453 (ptmm) cc_final: 0.8224 (ptmm) REVERT: A 141 ARG cc_start: 0.7558 (mtm180) cc_final: 0.6874 (mmm160) REVERT: A 285 LYS cc_start: 0.7999 (mttp) cc_final: 0.7755 (mmtt) REVERT: A 568 LYS cc_start: 0.8112 (tptp) cc_final: 0.7532 (mttt) REVERT: B 141 ARG cc_start: 0.7517 (mtm180) cc_final: 0.6854 (mmm160) REVERT: B 285 LYS cc_start: 0.8026 (mttp) cc_final: 0.7718 (mtpt) REVERT: B 431 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7509 (mtt90) REVERT: B 568 LYS cc_start: 0.8389 (mttt) cc_final: 0.7960 (mtmt) outliers start: 16 outliers final: 9 residues processed: 127 average time/residue: 0.3009 time to fit residues: 49.0315 Evaluate side-chains 122 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 431 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 352 GLN A 434 HIS A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9018 Z= 0.297 Angle : 0.574 6.855 12238 Z= 0.292 Chirality : 0.043 0.161 1454 Planarity : 0.004 0.037 1488 Dihedral : 8.990 87.212 1282 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.80 % Favored : 94.02 % Rotamer: Outliers : 1.77 % Allowed : 9.48 % Favored : 88.75 % 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: -2.07 (0.24), residues: 1104 helix: -0.51 (0.20), residues: 640 sheet: -1.45 (0.53), residues: 76 loop : -2.75 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 447 HIS 0.004 0.001 HIS B 434 PHE 0.015 0.001 PHE B 499 TYR 0.015 0.001 TYR A 594 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.051 Fit side-chains REVERT: A 133 LYS cc_start: 0.8444 (ptmm) cc_final: 0.8224 (ptmm) REVERT: A 141 ARG cc_start: 0.7515 (mtm180) cc_final: 0.6892 (mmm160) REVERT: A 237 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8922 (mt) REVERT: A 285 LYS cc_start: 0.7968 (mttp) cc_final: 0.7725 (mmtt) REVERT: A 568 LYS cc_start: 0.8098 (tptp) cc_final: 0.7528 (mttt) REVERT: B 141 ARG cc_start: 0.7526 (mtm180) cc_final: 0.6928 (mmm160) REVERT: B 237 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8919 (mt) REVERT: B 285 LYS cc_start: 0.8001 (mttp) cc_final: 0.7698 (mtpt) REVERT: B 568 LYS cc_start: 0.8411 (mttt) cc_final: 0.7953 (mtpt) outliers start: 17 outliers final: 14 residues processed: 131 average time/residue: 0.3013 time to fit residues: 51.0011 Evaluate side-chains 128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 277 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 454 ASN B 130 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9018 Z= 0.322 Angle : 0.589 6.795 12238 Z= 0.298 Chirality : 0.044 0.163 1454 Planarity : 0.004 0.038 1488 Dihedral : 8.990 86.141 1282 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.43 % Favored : 93.39 % Rotamer: Outliers : 1.77 % Allowed : 10.52 % Favored : 87.71 % 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: -1.88 (0.24), residues: 1104 helix: -0.35 (0.20), residues: 640 sheet: -1.47 (0.52), residues: 80 loop : -2.67 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 447 HIS 0.004 0.001 HIS B 434 PHE 0.015 0.001 PHE B 499 TYR 0.016 0.001 TYR A 152 ARG 0.003 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.942 Fit side-chains REVERT: A 141 ARG cc_start: 0.7506 (mtm180) cc_final: 0.6931 (mmm160) REVERT: A 237 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8941 (mt) REVERT: A 285 LYS cc_start: 0.7966 (mttp) cc_final: 0.7723 (mmtt) REVERT: A 568 LYS cc_start: 0.8131 (tptp) cc_final: 0.7533 (mttt) REVERT: B 141 ARG cc_start: 0.7500 (mtm180) cc_final: 0.6943 (mmm160) REVERT: B 237 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8938 (mt) REVERT: B 285 LYS cc_start: 0.7969 (mttp) cc_final: 0.7701 (mtpt) REVERT: B 568 LYS cc_start: 0.8388 (mttt) cc_final: 0.7933 (mtmt) outliers start: 17 outliers final: 15 residues processed: 128 average time/residue: 0.3112 time to fit residues: 51.5834 Evaluate side-chains 130 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 277 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 0.0030 overall best weight: 0.7692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9018 Z= 0.169 Angle : 0.508 6.775 12238 Z= 0.260 Chirality : 0.040 0.141 1454 Planarity : 0.003 0.037 1488 Dihedral : 8.407 81.720 1282 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 1.88 % Allowed : 10.83 % Favored : 87.29 % 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: -1.22 (0.25), residues: 1104 helix: 0.35 (0.21), residues: 624 sheet: -1.36 (0.52), residues: 76 loop : -2.56 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 447 HIS 0.003 0.001 HIS B 434 PHE 0.011 0.001 PHE A 499 TYR 0.014 0.001 TYR B 152 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.970 Fit side-chains REVERT: A 141 ARG cc_start: 0.7505 (mtm180) cc_final: 0.6930 (mmm160) REVERT: A 285 LYS cc_start: 0.7901 (mttp) cc_final: 0.7571 (mmtt) REVERT: A 402 ARG cc_start: 0.7435 (ttm170) cc_final: 0.6878 (mtt-85) REVERT: A 420 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7787 (mp) REVERT: A 568 LYS cc_start: 0.8126 (tptp) cc_final: 0.7517 (mtmt) REVERT: B 141 ARG cc_start: 0.7500 (mtm180) cc_final: 0.6932 (mmm160) REVERT: B 285 LYS cc_start: 0.7898 (mttp) cc_final: 0.7576 (mmtt) REVERT: B 402 ARG cc_start: 0.7439 (ttm170) cc_final: 0.6856 (mtt-85) REVERT: B 568 LYS cc_start: 0.8377 (mttt) cc_final: 0.7930 (mtmt) outliers start: 18 outliers final: 13 residues processed: 134 average time/residue: 0.3029 time to fit residues: 51.9774 Evaluate side-chains 135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 0.0270 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9018 Z= 0.258 Angle : 0.554 6.687 12238 Z= 0.281 Chirality : 0.042 0.153 1454 Planarity : 0.003 0.037 1488 Dihedral : 8.673 85.871 1282 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 1.77 % Allowed : 10.94 % Favored : 87.29 % 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: -1.18 (0.25), residues: 1104 helix: 0.27 (0.21), residues: 636 sheet: -1.17 (0.54), residues: 76 loop : -2.46 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 447 HIS 0.005 0.001 HIS B 434 PHE 0.013 0.001 PHE B 499 TYR 0.016 0.001 TYR B 152 ARG 0.003 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.017 Fit side-chains REVERT: A 141 ARG cc_start: 0.7496 (mtm180) cc_final: 0.6940 (mmm160) REVERT: A 285 LYS cc_start: 0.7938 (mttp) cc_final: 0.7611 (mttt) REVERT: A 402 ARG cc_start: 0.7445 (ttm170) cc_final: 0.6878 (mtt-85) REVERT: A 420 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7776 (mp) REVERT: A 568 LYS cc_start: 0.8138 (tptp) cc_final: 0.7515 (mtmt) REVERT: B 141 ARG cc_start: 0.7492 (mtm180) cc_final: 0.6948 (mmm160) REVERT: B 285 LYS cc_start: 0.7938 (mttp) cc_final: 0.7663 (mtpt) REVERT: B 402 ARG cc_start: 0.7454 (ttm170) cc_final: 0.6857 (mtt-85) REVERT: B 420 LEU cc_start: 0.8184 (tp) cc_final: 0.7927 (tp) REVERT: B 568 LYS cc_start: 0.8413 (mttt) cc_final: 0.7937 (mtpt) outliers start: 17 outliers final: 14 residues processed: 132 average time/residue: 0.3117 time to fit residues: 52.5396 Evaluate side-chains 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 0.0270 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 0.1980 chunk 103 optimal weight: 2.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9018 Z= 0.142 Angle : 0.495 6.727 12238 Z= 0.253 Chirality : 0.040 0.137 1454 Planarity : 0.003 0.033 1488 Dihedral : 8.140 80.614 1282 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.53 % Favored : 94.29 % Rotamer: Outliers : 1.88 % Allowed : 11.46 % 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: -0.67 (0.25), residues: 1104 helix: 0.81 (0.22), residues: 624 sheet: -1.10 (0.55), residues: 80 loop : -2.38 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 447 HIS 0.005 0.001 HIS B 434 PHE 0.011 0.001 PHE B 42 TYR 0.013 0.001 TYR B 152 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.184 Fit side-chains REVERT: A 141 ARG cc_start: 0.7489 (mtm180) cc_final: 0.6929 (mmm160) REVERT: A 285 LYS cc_start: 0.7865 (mttp) cc_final: 0.7545 (mmtt) REVERT: A 402 ARG cc_start: 0.7377 (ttm170) cc_final: 0.6894 (mtt-85) REVERT: A 420 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7790 (mp) REVERT: A 568 LYS cc_start: 0.8115 (tptp) cc_final: 0.7502 (mtmt) REVERT: B 141 ARG cc_start: 0.7475 (mtm180) cc_final: 0.6925 (mmm160) REVERT: B 285 LYS cc_start: 0.7881 (mttp) cc_final: 0.7559 (mmtt) REVERT: B 402 ARG cc_start: 0.7403 (ttm170) cc_final: 0.6906 (mtt-85) REVERT: B 568 LYS cc_start: 0.8385 (mttt) cc_final: 0.7933 (mtpt) outliers start: 18 outliers final: 15 residues processed: 139 average time/residue: 0.3369 time to fit residues: 59.7496 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 434 HIS A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9018 Z= 0.251 Angle : 0.549 6.622 12238 Z= 0.278 Chirality : 0.042 0.152 1454 Planarity : 0.003 0.035 1488 Dihedral : 8.589 86.552 1282 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.34 % Favored : 94.47 % Rotamer: Outliers : 1.88 % Allowed : 11.46 % 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: -0.92 (0.25), residues: 1104 helix: 0.57 (0.21), residues: 636 sheet: -0.93 (0.57), residues: 76 loop : -2.55 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 447 HIS 0.005 0.001 HIS A 434 PHE 0.013 0.001 PHE B 499 TYR 0.021 0.001 TYR B 152 ARG 0.006 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.994 Fit side-chains REVERT: A 141 ARG cc_start: 0.7488 (mtm180) cc_final: 0.6941 (mmm160) REVERT: A 285 LYS cc_start: 0.7911 (mttp) cc_final: 0.7578 (mmtt) REVERT: A 402 ARG cc_start: 0.7432 (ttm170) cc_final: 0.6897 (mtt-85) REVERT: A 420 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7785 (mp) REVERT: A 568 LYS cc_start: 0.8141 (tptp) cc_final: 0.7542 (mttt) REVERT: B 141 ARG cc_start: 0.7488 (mtm180) cc_final: 0.6950 (mmm160) REVERT: B 285 LYS cc_start: 0.7924 (mttp) cc_final: 0.7604 (mmtt) REVERT: B 402 ARG cc_start: 0.7442 (ttm170) cc_final: 0.6902 (mtt-85) REVERT: B 420 LEU cc_start: 0.8046 (tp) cc_final: 0.7726 (mp) REVERT: B 568 LYS cc_start: 0.8412 (mttt) cc_final: 0.7941 (mtpt) outliers start: 18 outliers final: 15 residues processed: 134 average time/residue: 0.3099 time to fit residues: 52.6021 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0040 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 434 HIS A 454 ASN A 662 HIS B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9018 Z= 0.148 Angle : 0.497 6.588 12238 Z= 0.254 Chirality : 0.040 0.141 1454 Planarity : 0.003 0.033 1488 Dihedral : 8.093 80.346 1282 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 1.88 % Allowed : 11.25 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.46 (0.26), residues: 1104 helix: 0.96 (0.22), residues: 624 sheet: -0.86 (0.56), residues: 80 loop : -2.29 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 447 HIS 0.004 0.001 HIS B 434 PHE 0.011 0.001 PHE A 499 TYR 0.018 0.001 TYR B 152 ARG 0.003 0.000 ARG B 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.009 Fit side-chains REVERT: A 141 ARG cc_start: 0.7482 (mtm180) cc_final: 0.6930 (mmm160) REVERT: A 285 LYS cc_start: 0.7827 (mttp) cc_final: 0.7513 (mmtt) REVERT: A 401 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7502 (ptp-170) REVERT: A 402 ARG cc_start: 0.7405 (ttm170) cc_final: 0.6986 (mtt-85) REVERT: A 420 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7816 (mp) REVERT: A 568 LYS cc_start: 0.8045 (tptp) cc_final: 0.7445 (mtmt) REVERT: B 141 ARG cc_start: 0.7479 (mtm180) cc_final: 0.6930 (mmm160) REVERT: B 285 LYS cc_start: 0.7860 (mttp) cc_final: 0.7545 (mmtt) REVERT: B 401 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7505 (ptp-170) REVERT: B 402 ARG cc_start: 0.7403 (ttm170) cc_final: 0.6956 (mtt-85) REVERT: B 568 LYS cc_start: 0.8429 (mttt) cc_final: 0.7956 (mtpt) outliers start: 18 outliers final: 15 residues processed: 138 average time/residue: 0.3127 time to fit residues: 54.9532 Evaluate side-chains 144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 0.0670 chunk 13 optimal weight: 0.0030 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 0.4928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 434 HIS A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.141475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.103115 restraints weight = 9054.738| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.89 r_work: 0.2920 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9018 Z= 0.133 Angle : 0.486 6.514 12238 Z= 0.248 Chirality : 0.039 0.135 1454 Planarity : 0.003 0.035 1488 Dihedral : 7.790 78.838 1282 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.43 % Favored : 94.38 % Rotamer: Outliers : 1.77 % Allowed : 11.46 % Favored : 86.77 % 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: -0.24 (0.26), residues: 1104 helix: 1.15 (0.22), residues: 628 sheet: -0.66 (0.57), residues: 80 loop : -2.27 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 447 HIS 0.004 0.001 HIS A 434 PHE 0.011 0.001 PHE A 499 TYR 0.018 0.001 TYR A 152 ARG 0.003 0.000 ARG B 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2138.86 seconds wall clock time: 39 minutes 40.00 seconds (2380.00 seconds total)