Starting phenix.real_space_refine on Sat Feb 17 15:01:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6boa_7122/02_2024/6boa_7122.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6boa_7122/02_2024/6boa_7122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6boa_7122/02_2024/6boa_7122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6boa_7122/02_2024/6boa_7122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6boa_7122/02_2024/6boa_7122.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6boa_7122/02_2024/6boa_7122.pdb" } resolution = 4.2 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= 0.002 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 12300 2.51 5 N 3208 2.21 5 O 3376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 621": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 621": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19040 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4760 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "B" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4760 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "C" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4760 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "D" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4760 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Time building chain proxies: 10.43, per 1000 atoms: 0.55 Number of scatterers: 19040 At special positions: 0 Unit cell: (139.7, 139.7, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 3376 8.00 N 3208 7.00 C 12300 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 - 3.50 Amino acid : False - 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: 7.59 Conformation dependent library (CDL) restraints added in 3.4 seconds 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 61.9% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 4.034A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.710A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.580A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.861A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.556A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.790A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.158A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.625A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.755A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.720A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.807A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 349 removed outlier: 3.649A pdb=" N ILE A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 403 removed outlier: 4.011A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 446 removed outlier: 3.529A pdb=" N ALA A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.558A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 480 through 486 removed outlier: 3.773A pdb=" N MET A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 512 removed outlier: 4.489A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.662A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.663A pdb=" N LEU A 530 " --> pdb=" O TYR A 526 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 580 removed outlier: 3.587A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 607 removed outlier: 3.882A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 4.034A pdb=" N ARG B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.710A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.580A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.861A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.557A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.789A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 221 removed outlier: 4.158A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.625A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 removed outlier: 3.755A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.500A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.806A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 349 removed outlier: 3.648A pdb=" N ILE B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR B 349 " --> pdb=" O MET B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 403 removed outlier: 4.012A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 446 removed outlier: 3.529A pdb=" N ALA B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.559A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 467 No H-bonds generated for 'chain 'B' and resid 465 through 467' Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 480 through 486 removed outlier: 3.773A pdb=" N MET B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 512 removed outlier: 4.489A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 3.662A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.661A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 580 removed outlier: 3.586A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B 571 " --> pdb=" O THR B 567 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 607 removed outlier: 3.881A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 4.034A pdb=" N ARG C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.710A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.580A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.861A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.556A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.790A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 212 through 221 removed outlier: 4.157A pdb=" N TYR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.625A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 298 removed outlier: 3.756A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.500A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.807A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 349 removed outlier: 3.649A pdb=" N ILE C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR C 349 " --> pdb=" O MET C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 403 removed outlier: 4.012A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 446 removed outlier: 3.529A pdb=" N ALA C 433 " --> pdb=" O ILE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.559A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 467 No H-bonds generated for 'chain 'C' and resid 465 through 467' Processing helix chain 'C' and resid 468 through 473 Processing helix chain 'C' and resid 480 through 486 removed outlier: 3.773A pdb=" N MET C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 512 removed outlier: 4.489A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 3.661A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.663A pdb=" N LEU C 530 " --> pdb=" O TYR C 526 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 580 removed outlier: 3.586A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU C 571 " --> pdb=" O THR C 567 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 607 removed outlier: 3.882A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLU C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE C 597 " --> pdb=" O TRP C 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 4.033A pdb=" N ARG D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.710A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.580A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.861A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.557A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.790A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 212 through 221 removed outlier: 4.158A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.626A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 298 removed outlier: 3.755A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.500A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.806A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 349 removed outlier: 3.649A pdb=" N ILE D 335 " --> pdb=" O MET D 331 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR D 349 " --> pdb=" O MET D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 403 removed outlier: 4.012A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 390 " --> pdb=" O LEU D 386 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 446 removed outlier: 3.529A pdb=" N ALA D 433 " --> pdb=" O ILE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.559A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN D 464 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 468 through 473 Processing helix chain 'D' and resid 480 through 486 removed outlier: 3.774A pdb=" N MET D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 512 removed outlier: 4.489A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA D 505 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 3.661A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.662A pdb=" N LEU D 530 " --> pdb=" O TYR D 526 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 580 removed outlier: 3.586A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 607 removed outlier: 3.882A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE D 597 " --> pdb=" O TRP D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 removed outlier: 3.586A pdb=" N LEU A 631 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.585A pdb=" N LEU B 631 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 270 removed outlier: 3.586A pdb=" N LEU C 631 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 269 through 270 removed outlier: 3.585A pdb=" N LEU D 631 " --> pdb=" O TYR D 278 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2292 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: 5.76 Time building geometry restraints manager: 8.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6066 1.34 - 1.46: 3998 1.46 - 1.58: 9148 1.58 - 1.70: 0 1.70 - 1.81: 264 Bond restraints: 19476 Sorted by residual: bond pdb=" CA HIS A 265 " pdb=" CB HIS A 265 " ideal model delta sigma weight residual 1.526 1.486 0.040 1.70e-02 3.46e+03 5.59e+00 bond pdb=" CA HIS B 265 " pdb=" CB HIS B 265 " ideal model delta sigma weight residual 1.526 1.486 0.040 1.70e-02 3.46e+03 5.59e+00 bond pdb=" CA HIS D 265 " pdb=" CB HIS D 265 " ideal model delta sigma weight residual 1.526 1.486 0.040 1.70e-02 3.46e+03 5.47e+00 bond pdb=" CA HIS C 265 " pdb=" CB HIS C 265 " ideal model delta sigma weight residual 1.526 1.486 0.040 1.70e-02 3.46e+03 5.44e+00 bond pdb=" C ARG D 350 " pdb=" N PRO D 351 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.07e+00 ... (remaining 19471 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.24: 567 106.24 - 113.54: 10755 113.54 - 120.83: 9391 120.83 - 128.13: 5495 128.13 - 135.42: 224 Bond angle restraints: 26432 Sorted by residual: angle pdb=" N MET C 554 " pdb=" CA MET C 554 " pdb=" C MET C 554 " ideal model delta sigma weight residual 114.75 105.37 9.38 1.26e+00 6.30e-01 5.54e+01 angle pdb=" N MET D 554 " pdb=" CA MET D 554 " pdb=" C MET D 554 " ideal model delta sigma weight residual 114.75 105.40 9.35 1.26e+00 6.30e-01 5.51e+01 angle pdb=" N MET A 554 " pdb=" CA MET A 554 " pdb=" C MET A 554 " ideal model delta sigma weight residual 114.75 105.43 9.32 1.26e+00 6.30e-01 5.47e+01 angle pdb=" N MET B 554 " pdb=" CA MET B 554 " pdb=" C MET B 554 " ideal model delta sigma weight residual 114.75 105.44 9.31 1.26e+00 6.30e-01 5.46e+01 angle pdb=" N LEU B 352 " pdb=" CA LEU B 352 " pdb=" C LEU B 352 " ideal model delta sigma weight residual 110.91 119.41 -8.50 1.17e+00 7.31e-01 5.28e+01 ... (remaining 26427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 10801 16.00 - 32.01: 657 32.01 - 48.01: 194 48.01 - 64.02: 4 64.02 - 80.02: 24 Dihedral angle restraints: 11680 sinusoidal: 4720 harmonic: 6960 Sorted by residual: dihedral pdb=" CA GLY B 476 " pdb=" C GLY B 476 " pdb=" N PRO B 477 " pdb=" CA PRO B 477 " ideal model delta harmonic sigma weight residual -180.00 -138.92 -41.08 0 5.00e+00 4.00e-02 6.75e+01 dihedral pdb=" CA GLY D 476 " pdb=" C GLY D 476 " pdb=" N PRO D 477 " pdb=" CA PRO D 477 " ideal model delta harmonic sigma weight residual 180.00 -138.93 -41.07 0 5.00e+00 4.00e-02 6.75e+01 dihedral pdb=" CA GLY A 476 " pdb=" C GLY A 476 " pdb=" N PRO A 477 " pdb=" CA PRO A 477 " ideal model delta harmonic sigma weight residual -180.00 -138.94 -41.06 0 5.00e+00 4.00e-02 6.74e+01 ... (remaining 11677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2266 0.060 - 0.121: 610 0.121 - 0.181: 96 0.181 - 0.241: 24 0.241 - 0.302: 16 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CB VAL D 452 " pdb=" CA VAL D 452 " pdb=" CG1 VAL D 452 " pdb=" CG2 VAL D 452 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB VAL A 452 " pdb=" CA VAL A 452 " pdb=" CG1 VAL A 452 " pdb=" CG2 VAL A 452 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB VAL B 452 " pdb=" CA VAL B 452 " pdb=" CG1 VAL B 452 " pdb=" CG2 VAL B 452 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 3009 not shown) Planarity restraints: 3336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 582 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C HIS C 582 " -0.043 2.00e-02 2.50e+03 pdb=" O HIS C 582 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP C 583 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 582 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C HIS B 582 " -0.043 2.00e-02 2.50e+03 pdb=" O HIS B 582 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP B 583 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 582 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C HIS D 582 " 0.043 2.00e-02 2.50e+03 pdb=" O HIS D 582 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP D 583 " -0.014 2.00e-02 2.50e+03 ... (remaining 3333 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5598 2.82 - 3.34: 17973 3.34 - 3.86: 29160 3.86 - 4.38: 33836 4.38 - 4.90: 55257 Nonbonded interactions: 141824 Sorted by model distance: nonbonded pdb=" O ASP A 284 " pdb=" OG SER A 291 " model vdw 2.296 2.440 nonbonded pdb=" O ASP D 284 " pdb=" OG SER D 291 " model vdw 2.296 2.440 nonbonded pdb=" O ASP C 284 " pdb=" OG SER C 291 " model vdw 2.297 2.440 nonbonded pdb=" O ASP B 284 " pdb=" OG SER B 291 " model vdw 2.297 2.440 nonbonded pdb=" OH TYR B 339 " pdb=" O THR B 392 " model vdw 2.345 2.440 ... (remaining 141819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.560 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: 3.110 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 51.570 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.007 0.069 19476 Z= 0.455 Angle : 1.289 19.123 26432 Z= 0.723 Chirality : 0.060 0.302 3012 Planarity : 0.008 0.061 3336 Dihedral : 11.912 80.021 7176 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 1.74 % Allowed : 5.23 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.53 % 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: -5.87 (0.11), residues: 2356 helix: -4.01 (0.07), residues: 1344 sheet: -4.97 (0.27), residues: 76 loop : -3.34 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP D 629 HIS 0.015 0.002 HIS D 522 PHE 0.039 0.003 PHE B 162 TYR 0.019 0.003 TYR B 270 ARG 0.010 0.001 ARG D 615 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 746 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.8200 (mmt90) cc_final: 0.7923 (mmt90) REVERT: A 96 MET cc_start: 0.8724 (mmm) cc_final: 0.8485 (mpp) REVERT: A 168 SER cc_start: 0.9510 (m) cc_final: 0.9301 (p) REVERT: A 178 ILE cc_start: 0.9214 (mp) cc_final: 0.8428 (mm) REVERT: A 197 ASN cc_start: 0.9080 (m-40) cc_final: 0.8747 (m110) REVERT: A 250 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8635 (mm-30) REVERT: A 332 LEU cc_start: 0.9373 (tp) cc_final: 0.9038 (tt) REVERT: A 434 PHE cc_start: 0.8502 (t80) cc_final: 0.8168 (t80) REVERT: A 437 LEU cc_start: 0.9191 (mp) cc_final: 0.8312 (mp) REVERT: A 453 PRO cc_start: 0.9560 (Cg_exo) cc_final: 0.9210 (Cg_endo) REVERT: A 539 THR cc_start: 0.9079 (m) cc_final: 0.8842 (p) REVERT: A 578 MET cc_start: 0.9186 (tpp) cc_final: 0.8938 (tpp) REVERT: A 603 MET cc_start: 0.8089 (ttp) cc_final: 0.7846 (ttt) REVERT: A 607 LYS cc_start: 0.8652 (mttp) cc_final: 0.8415 (mtmt) REVERT: B 75 ARG cc_start: 0.8166 (mmt90) cc_final: 0.7749 (mmt90) REVERT: B 96 MET cc_start: 0.8709 (mmm) cc_final: 0.8403 (mmm) REVERT: B 168 SER cc_start: 0.9523 (m) cc_final: 0.9161 (p) REVERT: B 197 ASN cc_start: 0.9145 (m-40) cc_final: 0.8766 (m110) REVERT: B 250 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8644 (mm-30) REVERT: B 294 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7978 (mp0) REVERT: B 316 LEU cc_start: 0.9407 (tp) cc_final: 0.9203 (tt) REVERT: B 331 MET cc_start: 0.7263 (tmm) cc_final: 0.6785 (tmm) REVERT: B 332 LEU cc_start: 0.9196 (tp) cc_final: 0.8892 (tt) REVERT: B 339 TYR cc_start: 0.8633 (t80) cc_final: 0.8035 (t80) REVERT: B 347 CYS cc_start: 0.8155 (t) cc_final: 0.7336 (t) REVERT: B 389 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7100 (tp30) REVERT: B 394 ILE cc_start: 0.9434 (mt) cc_final: 0.9194 (pt) REVERT: B 432 TYR cc_start: 0.9495 (t80) cc_final: 0.9213 (t80) REVERT: B 434 PHE cc_start: 0.8494 (t80) cc_final: 0.8155 (t80) REVERT: B 479 THR cc_start: 0.4269 (OUTLIER) cc_final: 0.3912 (t) REVERT: B 559 TYR cc_start: 0.9232 (t80) cc_final: 0.8962 (t80) REVERT: B 628 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8378 (mtm-85) REVERT: C 75 ARG cc_start: 0.8248 (mmt90) cc_final: 0.7879 (mmt90) REVERT: C 96 MET cc_start: 0.8799 (mmm) cc_final: 0.8502 (mmm) REVERT: C 150 THR cc_start: 0.8972 (m) cc_final: 0.8747 (t) REVERT: C 168 SER cc_start: 0.9508 (m) cc_final: 0.9126 (p) REVERT: C 197 ASN cc_start: 0.9178 (m-40) cc_final: 0.8804 (m110) REVERT: C 294 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7832 (mp0) REVERT: C 297 ILE cc_start: 0.9231 (pp) cc_final: 0.8964 (mm) REVERT: C 331 MET cc_start: 0.7201 (tmm) cc_final: 0.6952 (tmm) REVERT: C 332 LEU cc_start: 0.9292 (tp) cc_final: 0.9000 (tt) REVERT: C 339 TYR cc_start: 0.8576 (t80) cc_final: 0.7999 (t80) REVERT: C 347 CYS cc_start: 0.8074 (t) cc_final: 0.7379 (t) REVERT: C 389 GLU cc_start: 0.7285 (tm-30) cc_final: 0.7060 (tp30) REVERT: C 434 PHE cc_start: 0.8305 (t80) cc_final: 0.8082 (t80) REVERT: C 456 PHE cc_start: 0.8655 (m-10) cc_final: 0.8296 (m-10) REVERT: C 607 LYS cc_start: 0.8747 (mttp) cc_final: 0.8452 (mtmt) REVERT: C 628 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8313 (mtm-85) REVERT: D 96 MET cc_start: 0.8838 (mmm) cc_final: 0.8540 (mmm) REVERT: D 197 ASN cc_start: 0.9142 (m-40) cc_final: 0.8699 (m110) REVERT: D 241 LEU cc_start: 0.8808 (mt) cc_final: 0.8456 (mp) REVERT: D 250 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8657 (mm-30) REVERT: D 294 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8017 (mp0) REVERT: D 306 GLN cc_start: 0.9172 (tp-100) cc_final: 0.8848 (tp40) REVERT: D 332 LEU cc_start: 0.9277 (tp) cc_final: 0.9019 (tt) REVERT: D 336 TYR cc_start: 0.8936 (t80) cc_final: 0.8504 (t80) REVERT: D 342 CYS cc_start: 0.9165 (t) cc_final: 0.8874 (t) REVERT: D 347 CYS cc_start: 0.8225 (t) cc_final: 0.7545 (t) REVERT: D 394 ILE cc_start: 0.9396 (mt) cc_final: 0.9183 (pt) REVERT: D 434 PHE cc_start: 0.8345 (t80) cc_final: 0.7982 (t80) REVERT: D 456 PHE cc_start: 0.8888 (m-10) cc_final: 0.8589 (m-10) REVERT: D 578 MET cc_start: 0.9287 (tpp) cc_final: 0.8747 (tpp) REVERT: D 607 LYS cc_start: 0.8658 (mttp) cc_final: 0.8280 (mtmt) outliers start: 36 outliers final: 10 residues processed: 762 average time/residue: 0.3144 time to fit residues: 360.9865 Evaluate side-chains 457 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 446 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 174 ASN A 206 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS B 62 ASN B 118 GLN B 174 ASN B 206 GLN B 357 ASN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS C 118 GLN C 174 ASN C 206 GLN C 357 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS D 118 GLN D 174 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN D 464 ASN D 582 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19476 Z= 0.307 Angle : 0.831 14.643 26432 Z= 0.421 Chirality : 0.045 0.192 3012 Planarity : 0.005 0.039 3336 Dihedral : 6.306 32.003 2592 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.36 % Favored : 89.60 % Rotamer: Outliers : 0.48 % Allowed : 5.28 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.09 % 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: -3.48 (0.15), residues: 2356 helix: -1.71 (0.12), residues: 1352 sheet: -4.60 (0.32), residues: 76 loop : -2.90 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 593 HIS 0.002 0.001 HIS C 122 PHE 0.023 0.002 PHE A 472 TYR 0.013 0.002 TYR D 524 ARG 0.005 0.001 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 548 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8731 (tp) cc_final: 0.8451 (tp) REVERT: A 61 LEU cc_start: 0.8384 (mt) cc_final: 0.8009 (mt) REVERT: A 96 MET cc_start: 0.8584 (mmm) cc_final: 0.8135 (mmm) REVERT: A 197 ASN cc_start: 0.9118 (m-40) cc_final: 0.8653 (m110) REVERT: A 204 ILE cc_start: 0.9661 (OUTLIER) cc_final: 0.9361 (mp) REVERT: A 211 PHE cc_start: 0.8227 (t80) cc_final: 0.7752 (t80) REVERT: A 260 MET cc_start: 0.8676 (tpp) cc_final: 0.8468 (tpt) REVERT: A 332 LEU cc_start: 0.9101 (tp) cc_final: 0.8832 (tt) REVERT: A 363 ARG cc_start: 0.8739 (mtt180) cc_final: 0.8294 (mtp180) REVERT: A 434 PHE cc_start: 0.8400 (t80) cc_final: 0.8020 (t80) REVERT: A 437 LEU cc_start: 0.9286 (mp) cc_final: 0.8979 (tt) REVERT: A 497 MET cc_start: 0.8535 (ptp) cc_final: 0.8211 (ttp) REVERT: A 501 ILE cc_start: 0.9557 (tt) cc_final: 0.9237 (tp) REVERT: A 515 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7967 (mm-30) REVERT: A 539 THR cc_start: 0.9173 (m) cc_final: 0.8929 (p) REVERT: A 578 MET cc_start: 0.9069 (tpp) cc_final: 0.8705 (tpp) REVERT: A 602 VAL cc_start: 0.9302 (t) cc_final: 0.8920 (p) REVERT: A 607 LYS cc_start: 0.8560 (mttp) cc_final: 0.8172 (mtmt) REVERT: A 629 TRP cc_start: 0.7046 (m-10) cc_final: 0.6822 (m-10) REVERT: B 35 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8568 (mp0) REVERT: B 38 LEU cc_start: 0.8632 (tp) cc_final: 0.8390 (tp) REVERT: B 96 MET cc_start: 0.8627 (mmm) cc_final: 0.8304 (mmm) REVERT: B 197 ASN cc_start: 0.9171 (m-40) cc_final: 0.8696 (m110) REVERT: B 204 ILE cc_start: 0.9597 (OUTLIER) cc_final: 0.9305 (mp) REVERT: B 211 PHE cc_start: 0.8314 (t80) cc_final: 0.7754 (t80) REVERT: B 294 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8171 (mp0) REVERT: B 331 MET cc_start: 0.7066 (tmm) cc_final: 0.6787 (tmm) REVERT: B 332 LEU cc_start: 0.9135 (tp) cc_final: 0.8759 (tt) REVERT: B 339 TYR cc_start: 0.8497 (t80) cc_final: 0.8167 (t80) REVERT: B 432 TYR cc_start: 0.9342 (t80) cc_final: 0.9002 (t80) REVERT: B 501 ILE cc_start: 0.9406 (tt) cc_final: 0.9114 (tp) REVERT: B 578 MET cc_start: 0.8526 (tpp) cc_final: 0.8201 (tpp) REVERT: B 607 LYS cc_start: 0.8708 (mttp) cc_final: 0.8429 (mtmt) REVERT: C 35 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8610 (mp0) REVERT: C 40 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8842 (tm-30) REVERT: C 61 LEU cc_start: 0.8472 (mt) cc_final: 0.8128 (mt) REVERT: C 75 ARG cc_start: 0.8237 (mmt90) cc_final: 0.7965 (mmt90) REVERT: C 96 MET cc_start: 0.8640 (mmm) cc_final: 0.8243 (mmm) REVERT: C 197 ASN cc_start: 0.9201 (m-40) cc_final: 0.8732 (m110) REVERT: C 294 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8232 (mp0) REVERT: C 305 ARG cc_start: 0.8695 (mmt180) cc_final: 0.8275 (mmt-90) REVERT: C 331 MET cc_start: 0.7111 (tmm) cc_final: 0.6831 (tmm) REVERT: C 332 LEU cc_start: 0.9097 (tp) cc_final: 0.8835 (tt) REVERT: C 339 TYR cc_start: 0.8579 (t80) cc_final: 0.8158 (t80) REVERT: C 342 CYS cc_start: 0.9176 (t) cc_final: 0.8871 (t) REVERT: C 383 ASP cc_start: 0.8570 (m-30) cc_final: 0.8297 (m-30) REVERT: C 386 LEU cc_start: 0.8881 (tp) cc_final: 0.8615 (pp) REVERT: C 442 MET cc_start: 0.8686 (ttm) cc_final: 0.8456 (ttm) REVERT: C 454 MET cc_start: 0.9097 (mmm) cc_final: 0.8872 (mmm) REVERT: C 497 MET cc_start: 0.8025 (ttp) cc_final: 0.7624 (ttm) REVERT: C 501 ILE cc_start: 0.9312 (tt) cc_final: 0.9015 (tp) REVERT: C 593 TRP cc_start: 0.8588 (t60) cc_final: 0.8381 (t60) REVERT: C 607 LYS cc_start: 0.8612 (mttp) cc_final: 0.8353 (mtmt) REVERT: D 35 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8586 (mp0) REVERT: D 40 GLN cc_start: 0.9312 (tm-30) cc_final: 0.8841 (tm-30) REVERT: D 61 LEU cc_start: 0.8444 (mt) cc_final: 0.8129 (mt) REVERT: D 96 MET cc_start: 0.8751 (mmm) cc_final: 0.8406 (mmm) REVERT: D 197 ASN cc_start: 0.9245 (m-40) cc_final: 0.8825 (m110) REVERT: D 204 ILE cc_start: 0.9587 (OUTLIER) cc_final: 0.9326 (mp) REVERT: D 215 MET cc_start: 0.8454 (mpp) cc_final: 0.8223 (mpp) REVERT: D 331 MET cc_start: 0.7141 (tmm) cc_final: 0.6787 (tmm) REVERT: D 332 LEU cc_start: 0.9035 (tp) cc_final: 0.8743 (tt) REVERT: D 437 LEU cc_start: 0.9111 (mp) cc_final: 0.8790 (tt) REVERT: D 466 MET cc_start: 0.8293 (ttm) cc_final: 0.7699 (tmm) REVERT: D 497 MET cc_start: 0.8221 (ttp) cc_final: 0.7804 (ttm) REVERT: D 501 ILE cc_start: 0.9432 (tt) cc_final: 0.9155 (tp) REVERT: D 607 LYS cc_start: 0.8525 (mttp) cc_final: 0.8217 (mtmt) outliers start: 10 outliers final: 0 residues processed: 550 average time/residue: 0.2926 time to fit residues: 245.8249 Evaluate side-chains 423 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 420 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 212 optimal weight: 0.0030 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN B 62 ASN B 257 GLN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 257 GLN C 464 ASN D 174 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19476 Z= 0.246 Angle : 0.769 14.329 26432 Z= 0.379 Chirality : 0.044 0.176 3012 Planarity : 0.004 0.044 3336 Dihedral : 5.592 30.631 2592 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 0.19 % Allowed : 5.14 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -2.36 (0.17), residues: 2356 helix: -0.59 (0.14), residues: 1348 sheet: -4.07 (0.38), residues: 76 loop : -2.79 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 613 HIS 0.003 0.001 HIS B 122 PHE 0.016 0.002 PHE C 162 TYR 0.016 0.001 TYR C 324 ARG 0.006 0.000 ARG B 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 501 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8578 (tp) cc_final: 0.8349 (tp) REVERT: A 61 LEU cc_start: 0.8649 (mt) cc_final: 0.8250 (mt) REVERT: A 96 MET cc_start: 0.8599 (mmm) cc_final: 0.8201 (mmm) REVERT: A 197 ASN cc_start: 0.9154 (m-40) cc_final: 0.8758 (m110) REVERT: A 260 MET cc_start: 0.8649 (tpp) cc_final: 0.8433 (tpp) REVERT: A 363 ARG cc_start: 0.8762 (mtt180) cc_final: 0.8459 (ptm160) REVERT: A 434 PHE cc_start: 0.8382 (t80) cc_final: 0.7957 (t80) REVERT: A 437 LEU cc_start: 0.9277 (mp) cc_final: 0.8976 (tt) REVERT: A 539 THR cc_start: 0.9167 (m) cc_final: 0.8954 (p) REVERT: A 602 VAL cc_start: 0.9336 (t) cc_final: 0.8995 (p) REVERT: A 607 LYS cc_start: 0.8578 (mttp) cc_final: 0.8234 (mtmt) REVERT: A 629 TRP cc_start: 0.7225 (m-10) cc_final: 0.6991 (m-10) REVERT: B 35 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8545 (mp0) REVERT: B 38 LEU cc_start: 0.8544 (tp) cc_final: 0.8208 (tp) REVERT: B 96 MET cc_start: 0.8581 (mmm) cc_final: 0.8373 (mmm) REVERT: B 197 ASN cc_start: 0.9256 (m-40) cc_final: 0.8851 (m110) REVERT: B 331 MET cc_start: 0.7172 (tmm) cc_final: 0.6797 (tmm) REVERT: B 332 LEU cc_start: 0.9102 (tp) cc_final: 0.8794 (tt) REVERT: B 339 TYR cc_start: 0.8510 (t80) cc_final: 0.8221 (t80) REVERT: B 432 TYR cc_start: 0.9351 (t80) cc_final: 0.9002 (t80) REVERT: B 437 LEU cc_start: 0.9015 (mp) cc_final: 0.8693 (tt) REVERT: B 442 MET cc_start: 0.8433 (ttm) cc_final: 0.8223 (ttm) REVERT: B 472 PHE cc_start: 0.6414 (t80) cc_final: 0.5960 (t80) REVERT: B 578 MET cc_start: 0.8652 (tpp) cc_final: 0.8316 (tpp) REVERT: B 602 VAL cc_start: 0.9487 (t) cc_final: 0.9157 (p) REVERT: B 607 LYS cc_start: 0.8636 (mttp) cc_final: 0.8328 (mtmt) REVERT: C 35 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8610 (mp0) REVERT: C 40 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8836 (tm-30) REVERT: C 61 LEU cc_start: 0.8551 (mt) cc_final: 0.8176 (mt) REVERT: C 75 ARG cc_start: 0.8225 (mmt90) cc_final: 0.7892 (mmt90) REVERT: C 96 MET cc_start: 0.8595 (mmm) cc_final: 0.8237 (mmm) REVERT: C 197 ASN cc_start: 0.9279 (m-40) cc_final: 0.8906 (m110) REVERT: C 305 ARG cc_start: 0.8717 (mmt180) cc_final: 0.8373 (mmt-90) REVERT: C 331 MET cc_start: 0.7236 (tmm) cc_final: 0.6847 (tmm) REVERT: C 332 LEU cc_start: 0.9067 (tp) cc_final: 0.8737 (tt) REVERT: C 339 TYR cc_start: 0.8546 (t80) cc_final: 0.8179 (t80) REVERT: C 472 PHE cc_start: 0.6494 (t80) cc_final: 0.6264 (t80) REVERT: C 497 MET cc_start: 0.8024 (ttp) cc_final: 0.7629 (ttm) REVERT: C 607 LYS cc_start: 0.8633 (mttp) cc_final: 0.8356 (mtmt) REVERT: D 35 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8563 (mp0) REVERT: D 38 LEU cc_start: 0.8632 (tp) cc_final: 0.8402 (tp) REVERT: D 61 LEU cc_start: 0.8562 (mt) cc_final: 0.8195 (mt) REVERT: D 75 ARG cc_start: 0.8225 (mmt90) cc_final: 0.7946 (mmt90) REVERT: D 96 MET cc_start: 0.8661 (mmm) cc_final: 0.8442 (mmm) REVERT: D 197 ASN cc_start: 0.9240 (m-40) cc_final: 0.8817 (m110) REVERT: D 215 MET cc_start: 0.8456 (mpp) cc_final: 0.8142 (mpp) REVERT: D 437 LEU cc_start: 0.9136 (mp) cc_final: 0.8842 (tt) REVERT: D 466 MET cc_start: 0.8337 (ttm) cc_final: 0.7636 (tmm) REVERT: D 602 VAL cc_start: 0.9269 (t) cc_final: 0.8926 (p) REVERT: D 607 LYS cc_start: 0.8587 (mttp) cc_final: 0.8242 (mtmt) outliers start: 4 outliers final: 0 residues processed: 501 average time/residue: 0.2996 time to fit residues: 227.6113 Evaluate side-chains 409 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 204 optimal weight: 0.0370 chunk 61 optimal weight: 3.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 174 ASN B 464 ASN C 464 ASN D 91 ASN D 206 GLN D 357 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19476 Z= 0.169 Angle : 0.707 14.149 26432 Z= 0.344 Chirality : 0.042 0.175 3012 Planarity : 0.004 0.044 3336 Dihedral : 5.175 30.048 2592 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.68 % Favored : 90.28 % Rotamer: Outliers : 0.10 % Allowed : 3.88 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -1.59 (0.17), residues: 2356 helix: 0.04 (0.15), residues: 1300 sheet: -3.59 (0.43), residues: 76 loop : -2.37 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 462 HIS 0.004 0.001 HIS C 201 PHE 0.017 0.001 PHE D 434 TYR 0.014 0.001 TYR B 270 ARG 0.006 0.000 ARG B 628 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 534 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8477 (tp) cc_final: 0.8108 (tp) REVERT: A 61 LEU cc_start: 0.8609 (mt) cc_final: 0.8183 (mt) REVERT: A 75 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7813 (mmt90) REVERT: A 96 MET cc_start: 0.8569 (mmm) cc_final: 0.8172 (mmm) REVERT: A 197 ASN cc_start: 0.9091 (m-40) cc_final: 0.8794 (m110) REVERT: A 217 ASN cc_start: 0.8897 (t0) cc_final: 0.8661 (t0) REVERT: A 363 ARG cc_start: 0.8711 (mtt180) cc_final: 0.8384 (ptm160) REVERT: A 434 PHE cc_start: 0.8336 (t80) cc_final: 0.7975 (t80) REVERT: A 437 LEU cc_start: 0.9173 (mp) cc_final: 0.8890 (tt) REVERT: A 442 MET cc_start: 0.8639 (ttm) cc_final: 0.8399 (ttm) REVERT: A 497 MET cc_start: 0.8099 (ttp) cc_final: 0.7614 (ttm) REVERT: A 520 LEU cc_start: 0.8597 (mt) cc_final: 0.8388 (mt) REVERT: A 550 ASP cc_start: 0.7962 (m-30) cc_final: 0.7734 (m-30) REVERT: A 589 ARG cc_start: 0.7300 (mmt180) cc_final: 0.6868 (mmt180) REVERT: A 602 VAL cc_start: 0.9333 (t) cc_final: 0.9010 (p) REVERT: A 607 LYS cc_start: 0.8486 (mttp) cc_final: 0.8188 (mtmt) REVERT: A 629 TRP cc_start: 0.7277 (m-10) cc_final: 0.7055 (m-10) REVERT: B 35 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8539 (mp0) REVERT: B 96 MET cc_start: 0.8602 (mmm) cc_final: 0.8190 (mmm) REVERT: B 197 ASN cc_start: 0.9161 (m-40) cc_final: 0.8828 (m110) REVERT: B 331 MET cc_start: 0.7152 (tmm) cc_final: 0.6762 (tmm) REVERT: B 332 LEU cc_start: 0.9051 (tp) cc_final: 0.8723 (tt) REVERT: B 339 TYR cc_start: 0.8532 (t80) cc_final: 0.8232 (t80) REVERT: B 472 PHE cc_start: 0.6282 (t80) cc_final: 0.5859 (t80) REVERT: B 497 MET cc_start: 0.8039 (ttp) cc_final: 0.7472 (ttm) REVERT: B 501 ILE cc_start: 0.9416 (tt) cc_final: 0.9117 (tp) REVERT: B 602 VAL cc_start: 0.9417 (t) cc_final: 0.9088 (p) REVERT: B 607 LYS cc_start: 0.8644 (mttp) cc_final: 0.8352 (mtmt) REVERT: C 35 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8576 (mp0) REVERT: C 40 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8820 (tm-30) REVERT: C 61 LEU cc_start: 0.8564 (mt) cc_final: 0.8153 (mt) REVERT: C 96 MET cc_start: 0.8574 (mmm) cc_final: 0.8234 (mmm) REVERT: C 197 ASN cc_start: 0.9255 (m-40) cc_final: 0.8964 (m110) REVERT: C 305 ARG cc_start: 0.8682 (mmt180) cc_final: 0.8336 (mmt-90) REVERT: C 331 MET cc_start: 0.7207 (tmm) cc_final: 0.6815 (tmm) REVERT: C 339 TYR cc_start: 0.8573 (t80) cc_final: 0.8203 (t80) REVERT: C 428 LEU cc_start: 0.8416 (pp) cc_final: 0.8098 (pp) REVERT: C 472 PHE cc_start: 0.6368 (t80) cc_final: 0.6058 (t80) REVERT: C 497 MET cc_start: 0.7860 (ttp) cc_final: 0.7419 (ttm) REVERT: C 501 ILE cc_start: 0.9324 (tt) cc_final: 0.9025 (tp) REVERT: C 539 THR cc_start: 0.9034 (m) cc_final: 0.8730 (p) REVERT: C 607 LYS cc_start: 0.8631 (mttp) cc_final: 0.8323 (mtmt) REVERT: D 35 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8525 (mp0) REVERT: D 61 LEU cc_start: 0.8592 (mt) cc_final: 0.8190 (mt) REVERT: D 96 MET cc_start: 0.8647 (mmm) cc_final: 0.8219 (mmm) REVERT: D 339 TYR cc_start: 0.8631 (t80) cc_final: 0.8357 (t80) REVERT: D 466 MET cc_start: 0.8290 (ttm) cc_final: 0.7669 (tmm) REVERT: D 472 PHE cc_start: 0.6874 (t80) cc_final: 0.6559 (t80) REVERT: D 497 MET cc_start: 0.8128 (ttp) cc_final: 0.7638 (ttm) REVERT: D 501 ILE cc_start: 0.9339 (tt) cc_final: 0.9003 (tp) REVERT: D 578 MET cc_start: 0.7784 (ttm) cc_final: 0.7301 (ttm) REVERT: D 607 LYS cc_start: 0.8590 (mttp) cc_final: 0.8129 (mtmt) outliers start: 2 outliers final: 0 residues processed: 534 average time/residue: 0.2858 time to fit residues: 235.8262 Evaluate side-chains 435 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.5980 chunk 129 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 204 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 174 ASN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN C 174 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN D 257 GLN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19476 Z= 0.176 Angle : 0.709 14.781 26432 Z= 0.340 Chirality : 0.042 0.170 3012 Planarity : 0.004 0.043 3336 Dihedral : 4.924 30.096 2592 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -1.23 (0.18), residues: 2356 helix: 0.36 (0.15), residues: 1292 sheet: -3.17 (0.47), residues: 76 loop : -2.25 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 583 HIS 0.003 0.001 HIS A 201 PHE 0.017 0.001 PHE C 434 TYR 0.016 0.001 TYR D 336 ARG 0.007 0.000 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 523 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8459 (tp) cc_final: 0.8095 (tp) REVERT: A 61 LEU cc_start: 0.8686 (mt) cc_final: 0.8268 (mt) REVERT: A 92 LEU cc_start: 0.8701 (pt) cc_final: 0.8307 (pt) REVERT: A 96 MET cc_start: 0.8578 (mmm) cc_final: 0.8193 (mmm) REVERT: A 130 MET cc_start: 0.8271 (tpt) cc_final: 0.7540 (tpp) REVERT: A 217 ASN cc_start: 0.9020 (t0) cc_final: 0.8800 (t0) REVERT: A 363 ARG cc_start: 0.8675 (mtt180) cc_final: 0.8366 (ptm160) REVERT: A 434 PHE cc_start: 0.8325 (t80) cc_final: 0.7919 (t80) REVERT: A 437 LEU cc_start: 0.9116 (mp) cc_final: 0.8742 (tt) REVERT: A 497 MET cc_start: 0.8064 (ttp) cc_final: 0.7583 (ttm) REVERT: A 515 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8102 (mm-30) REVERT: A 520 LEU cc_start: 0.8661 (mt) cc_final: 0.8448 (mt) REVERT: A 589 ARG cc_start: 0.7210 (mmt180) cc_final: 0.6900 (mmt180) REVERT: A 602 VAL cc_start: 0.9336 (t) cc_final: 0.9020 (p) REVERT: A 607 LYS cc_start: 0.8504 (mttp) cc_final: 0.8072 (mtmt) REVERT: A 629 TRP cc_start: 0.7286 (m-10) cc_final: 0.6998 (m-10) REVERT: B 35 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8585 (mp0) REVERT: B 96 MET cc_start: 0.8537 (mmm) cc_final: 0.8211 (mmm) REVERT: B 332 LEU cc_start: 0.9105 (tp) cc_final: 0.8894 (tt) REVERT: B 339 TYR cc_start: 0.8516 (t80) cc_final: 0.8308 (t80) REVERT: B 363 ARG cc_start: 0.7760 (mmm160) cc_final: 0.7314 (mmm160) REVERT: B 472 PHE cc_start: 0.6629 (t80) cc_final: 0.6209 (t80) REVERT: B 497 MET cc_start: 0.8003 (ttp) cc_final: 0.7459 (ttm) REVERT: B 539 THR cc_start: 0.9072 (m) cc_final: 0.8756 (p) REVERT: B 602 VAL cc_start: 0.9410 (t) cc_final: 0.9098 (p) REVERT: B 607 LYS cc_start: 0.8668 (mttp) cc_final: 0.8358 (mtmt) REVERT: C 35 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8592 (mp0) REVERT: C 38 LEU cc_start: 0.8417 (tp) cc_final: 0.8196 (tp) REVERT: C 40 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8806 (tm-30) REVERT: C 61 LEU cc_start: 0.8591 (mt) cc_final: 0.8153 (mt) REVERT: C 92 LEU cc_start: 0.8730 (pt) cc_final: 0.8335 (pt) REVERT: C 113 GLU cc_start: 0.7746 (mp0) cc_final: 0.7506 (mp0) REVERT: C 130 MET cc_start: 0.8446 (tpt) cc_final: 0.7796 (tpp) REVERT: C 305 ARG cc_start: 0.8698 (mmt180) cc_final: 0.8362 (mmt-90) REVERT: C 339 TYR cc_start: 0.8516 (t80) cc_final: 0.8217 (t80) REVERT: C 363 ARG cc_start: 0.7575 (mmm160) cc_final: 0.7320 (mmm160) REVERT: C 472 PHE cc_start: 0.6634 (t80) cc_final: 0.6385 (t80) REVERT: C 501 ILE cc_start: 0.9283 (tt) cc_final: 0.9009 (tp) REVERT: C 607 LYS cc_start: 0.8623 (mttp) cc_final: 0.8290 (mtmt) REVERT: D 35 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8559 (mp0) REVERT: D 38 LEU cc_start: 0.8557 (tp) cc_final: 0.8087 (tt) REVERT: D 61 LEU cc_start: 0.8643 (mt) cc_final: 0.8212 (mt) REVERT: D 339 TYR cc_start: 0.8578 (t80) cc_final: 0.8295 (t80) REVERT: D 454 MET cc_start: 0.9118 (tpp) cc_final: 0.8793 (tpp) REVERT: D 466 MET cc_start: 0.8357 (ttm) cc_final: 0.7767 (tmm) REVERT: D 472 PHE cc_start: 0.6946 (t80) cc_final: 0.6630 (t80) REVERT: D 497 MET cc_start: 0.8110 (ttp) cc_final: 0.7662 (ttm) REVERT: D 501 ILE cc_start: 0.9369 (tt) cc_final: 0.9065 (tp) REVERT: D 515 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7675 (tp30) REVERT: D 607 LYS cc_start: 0.8599 (mttp) cc_final: 0.8171 (mtmt) outliers start: 2 outliers final: 0 residues processed: 525 average time/residue: 0.3118 time to fit residues: 252.1034 Evaluate side-chains 419 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 8.9990 chunk 205 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 228 optimal weight: 0.7980 chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19476 Z= 0.172 Angle : 0.691 14.859 26432 Z= 0.332 Chirality : 0.042 0.179 3012 Planarity : 0.004 0.045 3336 Dihedral : 4.774 28.924 2592 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % 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: -0.99 (0.18), residues: 2356 helix: 0.61 (0.15), residues: 1288 sheet: -2.91 (0.50), residues: 76 loop : -2.23 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 462 HIS 0.004 0.000 HIS B 587 PHE 0.019 0.001 PHE C 434 TYR 0.016 0.001 TYR C 336 ARG 0.006 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 529 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8450 (tp) cc_final: 0.8077 (tp) REVERT: A 61 LEU cc_start: 0.8700 (mt) cc_final: 0.8268 (mt) REVERT: A 92 LEU cc_start: 0.8707 (pt) cc_final: 0.8312 (pt) REVERT: A 113 GLU cc_start: 0.8089 (mp0) cc_final: 0.7832 (mp0) REVERT: A 130 MET cc_start: 0.8220 (tpt) cc_final: 0.7527 (tpp) REVERT: A 217 ASN cc_start: 0.8991 (t0) cc_final: 0.8780 (t0) REVERT: A 363 ARG cc_start: 0.8686 (mtt180) cc_final: 0.8393 (ptm160) REVERT: A 434 PHE cc_start: 0.8316 (t80) cc_final: 0.7922 (t80) REVERT: A 437 LEU cc_start: 0.9132 (mp) cc_final: 0.8791 (tt) REVERT: A 497 MET cc_start: 0.8035 (ttp) cc_final: 0.7586 (ttm) REVERT: A 515 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8111 (mm-30) REVERT: A 589 ARG cc_start: 0.7238 (mmt180) cc_final: 0.6937 (mmt180) REVERT: A 602 VAL cc_start: 0.9315 (t) cc_final: 0.9015 (p) REVERT: A 607 LYS cc_start: 0.8495 (mttp) cc_final: 0.8116 (mtmt) REVERT: A 629 TRP cc_start: 0.7361 (m-10) cc_final: 0.7067 (m-10) REVERT: B 35 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8580 (mp0) REVERT: B 78 MET cc_start: 0.8080 (ptp) cc_final: 0.7764 (ptp) REVERT: B 130 MET cc_start: 0.8169 (tpt) cc_final: 0.7313 (tpp) REVERT: B 216 TYR cc_start: 0.8929 (t80) cc_final: 0.8566 (t80) REVERT: B 363 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7300 (mmm160) REVERT: B 472 PHE cc_start: 0.6490 (t80) cc_final: 0.6200 (t80) REVERT: B 497 MET cc_start: 0.7887 (ttp) cc_final: 0.7321 (ttm) REVERT: B 539 THR cc_start: 0.9086 (m) cc_final: 0.8798 (p) REVERT: B 554 MET cc_start: 0.8839 (tpt) cc_final: 0.8624 (tpp) REVERT: B 570 MET cc_start: 0.8341 (ttm) cc_final: 0.7844 (tpp) REVERT: B 602 VAL cc_start: 0.9449 (t) cc_final: 0.9148 (p) REVERT: B 607 LYS cc_start: 0.8681 (mttp) cc_final: 0.8317 (mtmt) REVERT: C 35 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8586 (mp0) REVERT: C 61 LEU cc_start: 0.8689 (mt) cc_final: 0.8263 (mt) REVERT: C 96 MET cc_start: 0.8621 (mmm) cc_final: 0.8210 (mmt) REVERT: C 305 ARG cc_start: 0.8688 (mmt180) cc_final: 0.8339 (mmt-90) REVERT: C 339 TYR cc_start: 0.8502 (t80) cc_final: 0.8235 (t80) REVERT: C 363 ARG cc_start: 0.7606 (mmm160) cc_final: 0.7311 (mmm160) REVERT: C 386 LEU cc_start: 0.9263 (tp) cc_final: 0.8903 (pp) REVERT: C 454 MET cc_start: 0.9332 (tpt) cc_final: 0.8950 (tpt) REVERT: C 497 MET cc_start: 0.8028 (ttp) cc_final: 0.7739 (ttm) REVERT: C 501 ILE cc_start: 0.9255 (tt) cc_final: 0.8979 (tp) REVERT: C 607 LYS cc_start: 0.8636 (mttp) cc_final: 0.8290 (mtmt) REVERT: D 35 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8556 (mp0) REVERT: D 38 LEU cc_start: 0.8536 (tp) cc_final: 0.8257 (tp) REVERT: D 61 LEU cc_start: 0.8683 (mt) cc_final: 0.8259 (mt) REVERT: D 96 MET cc_start: 0.8786 (mmm) cc_final: 0.8367 (mmm) REVERT: D 113 GLU cc_start: 0.7971 (mp0) cc_final: 0.7708 (mp0) REVERT: D 116 GLU cc_start: 0.7795 (mp0) cc_final: 0.7355 (mp0) REVERT: D 130 MET cc_start: 0.8285 (tpt) cc_final: 0.7545 (tpp) REVERT: D 216 TYR cc_start: 0.8958 (t80) cc_final: 0.8613 (t80) REVERT: D 339 TYR cc_start: 0.8593 (t80) cc_final: 0.8309 (t80) REVERT: D 386 LEU cc_start: 0.9203 (tp) cc_final: 0.8895 (pp) REVERT: D 454 MET cc_start: 0.9046 (tpp) cc_final: 0.8730 (tpp) REVERT: D 466 MET cc_start: 0.8313 (ttm) cc_final: 0.7795 (tmm) REVERT: D 472 PHE cc_start: 0.6771 (t80) cc_final: 0.6567 (t80) REVERT: D 497 MET cc_start: 0.7798 (ttp) cc_final: 0.7425 (ttm) REVERT: D 607 LYS cc_start: 0.8634 (mttp) cc_final: 0.8212 (mtmt) outliers start: 3 outliers final: 0 residues processed: 532 average time/residue: 0.2819 time to fit residues: 232.6657 Evaluate side-chains 428 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 192 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 227 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 174 ASN C 258 HIS ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19476 Z= 0.189 Angle : 0.701 15.174 26432 Z= 0.336 Chirality : 0.042 0.170 3012 Planarity : 0.004 0.044 3336 Dihedral : 4.775 28.944 2592 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 0.19 % Allowed : 1.65 % Favored : 98.16 % 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: -0.79 (0.18), residues: 2356 helix: 0.78 (0.15), residues: 1288 sheet: -2.71 (0.54), residues: 76 loop : -2.17 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 583 HIS 0.002 0.001 HIS A 122 PHE 0.020 0.001 PHE C 434 TYR 0.019 0.001 TYR B 336 ARG 0.004 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 510 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8579 (mp0) REVERT: A 38 LEU cc_start: 0.8462 (tp) cc_final: 0.8110 (tp) REVERT: A 55 ASP cc_start: 0.8397 (t70) cc_final: 0.7848 (t70) REVERT: A 61 LEU cc_start: 0.8740 (mt) cc_final: 0.8262 (mt) REVERT: A 96 MET cc_start: 0.8721 (mmm) cc_final: 0.8364 (mmm) REVERT: A 113 GLU cc_start: 0.8015 (mp0) cc_final: 0.7769 (mp0) REVERT: A 217 ASN cc_start: 0.8925 (t0) cc_final: 0.8672 (t0) REVERT: A 363 ARG cc_start: 0.8665 (mtt180) cc_final: 0.8365 (ptm160) REVERT: A 434 PHE cc_start: 0.8314 (t80) cc_final: 0.7962 (t80) REVERT: A 437 LEU cc_start: 0.9141 (mp) cc_final: 0.8780 (tt) REVERT: A 454 MET cc_start: 0.9048 (tpp) cc_final: 0.8711 (tpp) REVERT: A 515 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8152 (mm-30) REVERT: A 570 MET cc_start: 0.8239 (ttm) cc_final: 0.8017 (tpp) REVERT: A 589 ARG cc_start: 0.7264 (mmt180) cc_final: 0.6950 (mmt180) REVERT: A 602 VAL cc_start: 0.9341 (t) cc_final: 0.9023 (p) REVERT: A 607 LYS cc_start: 0.8489 (mttp) cc_final: 0.8099 (mtmt) REVERT: A 629 TRP cc_start: 0.7583 (m-10) cc_final: 0.7355 (m-10) REVERT: B 35 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8544 (mp0) REVERT: B 62 ASN cc_start: 0.8558 (m-40) cc_final: 0.8206 (m-40) REVERT: B 78 MET cc_start: 0.8052 (ptp) cc_final: 0.7769 (ptp) REVERT: B 96 MET cc_start: 0.8622 (mmm) cc_final: 0.8164 (mmm) REVERT: B 363 ARG cc_start: 0.7805 (mmm160) cc_final: 0.7315 (mmm160) REVERT: B 472 PHE cc_start: 0.6543 (t80) cc_final: 0.6232 (t80) REVERT: B 481 MET cc_start: 0.7315 (tpp) cc_final: 0.7101 (tpt) REVERT: B 497 MET cc_start: 0.7857 (ttp) cc_final: 0.7372 (ttm) REVERT: B 570 MET cc_start: 0.8346 (ttm) cc_final: 0.7820 (tpp) REVERT: B 602 VAL cc_start: 0.9484 (t) cc_final: 0.9189 (p) REVERT: B 607 LYS cc_start: 0.8662 (mttp) cc_final: 0.8358 (mtmt) REVERT: C 35 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8622 (mp0) REVERT: C 40 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8776 (tm-30) REVERT: C 61 LEU cc_start: 0.8655 (mt) cc_final: 0.8231 (mt) REVERT: C 92 LEU cc_start: 0.8755 (pt) cc_final: 0.8316 (pt) REVERT: C 96 MET cc_start: 0.8657 (mmm) cc_final: 0.8291 (mmm) REVERT: C 113 GLU cc_start: 0.7826 (mp0) cc_final: 0.7588 (mp0) REVERT: C 130 MET cc_start: 0.8379 (tpt) cc_final: 0.7532 (tpp) REVERT: C 305 ARG cc_start: 0.8688 (mmt180) cc_final: 0.8343 (mmt-90) REVERT: C 339 TYR cc_start: 0.8539 (t80) cc_final: 0.8275 (t80) REVERT: C 363 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7426 (mmm160) REVERT: C 386 LEU cc_start: 0.9300 (tp) cc_final: 0.8925 (pp) REVERT: C 454 MET cc_start: 0.9356 (tpt) cc_final: 0.9033 (tpt) REVERT: C 472 PHE cc_start: 0.6936 (t80) cc_final: 0.6623 (t80) REVERT: C 497 MET cc_start: 0.8080 (ttp) cc_final: 0.7735 (ttm) REVERT: C 501 ILE cc_start: 0.9333 (tt) cc_final: 0.9040 (tp) REVERT: C 539 THR cc_start: 0.9241 (m) cc_final: 0.8957 (p) REVERT: C 593 TRP cc_start: 0.8757 (t60) cc_final: 0.8342 (t60) REVERT: C 602 VAL cc_start: 0.9384 (t) cc_final: 0.9109 (p) REVERT: C 607 LYS cc_start: 0.8683 (mttp) cc_final: 0.8302 (mtmt) REVERT: D 35 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8584 (mp0) REVERT: D 38 LEU cc_start: 0.8481 (tp) cc_final: 0.8172 (tp) REVERT: D 61 LEU cc_start: 0.8688 (mt) cc_final: 0.8245 (mt) REVERT: D 96 MET cc_start: 0.8749 (mmm) cc_final: 0.8295 (mmm) REVERT: D 116 GLU cc_start: 0.7793 (mp0) cc_final: 0.7538 (mp0) REVERT: D 130 MET cc_start: 0.8345 (tpt) cc_final: 0.7610 (tpp) REVERT: D 339 TYR cc_start: 0.8590 (t80) cc_final: 0.8308 (t80) REVERT: D 454 MET cc_start: 0.9070 (tpp) cc_final: 0.8736 (tpp) REVERT: D 466 MET cc_start: 0.8365 (ttm) cc_final: 0.7824 (tmm) REVERT: D 495 TRP cc_start: 0.8335 (t-100) cc_final: 0.8064 (t-100) REVERT: D 497 MET cc_start: 0.8071 (ttp) cc_final: 0.7633 (ttm) REVERT: D 515 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7690 (tp30) REVERT: D 590 ASP cc_start: 0.8553 (t0) cc_final: 0.8315 (t0) REVERT: D 593 TRP cc_start: 0.8936 (t60) cc_final: 0.8392 (t60) REVERT: D 602 VAL cc_start: 0.9360 (t) cc_final: 0.9053 (p) REVERT: D 607 LYS cc_start: 0.8632 (mttp) cc_final: 0.8242 (mtmt) outliers start: 4 outliers final: 0 residues processed: 514 average time/residue: 0.2812 time to fit residues: 224.4122 Evaluate side-chains 415 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN C 174 ASN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19476 Z= 0.170 Angle : 0.695 15.217 26432 Z= 0.331 Chirality : 0.042 0.170 3012 Planarity : 0.004 0.043 3336 Dihedral : 4.668 29.240 2592 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.19 % Allowed : 1.21 % Favored : 98.59 % 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: -0.71 (0.18), residues: 2356 helix: 0.91 (0.15), residues: 1272 sheet: -2.51 (0.55), residues: 76 loop : -2.19 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 583 HIS 0.002 0.000 HIS A 522 PHE 0.023 0.001 PHE C 434 TYR 0.020 0.001 TYR B 336 ARG 0.004 0.000 ARG C 628 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 504 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8443 (tp) cc_final: 0.8088 (tp) REVERT: A 55 ASP cc_start: 0.8457 (t70) cc_final: 0.7866 (t70) REVERT: A 61 LEU cc_start: 0.8668 (mt) cc_final: 0.8173 (mt) REVERT: A 92 LEU cc_start: 0.8572 (pt) cc_final: 0.7937 (pt) REVERT: A 96 MET cc_start: 0.8587 (mmm) cc_final: 0.8222 (mmm) REVERT: A 113 GLU cc_start: 0.7967 (mp0) cc_final: 0.7736 (mp0) REVERT: A 130 MET cc_start: 0.8067 (tpt) cc_final: 0.7497 (tpp) REVERT: A 217 ASN cc_start: 0.8877 (t0) cc_final: 0.8633 (t0) REVERT: A 363 ARG cc_start: 0.8665 (mtt180) cc_final: 0.8375 (ptm160) REVERT: A 434 PHE cc_start: 0.8246 (t80) cc_final: 0.7930 (t80) REVERT: A 437 LEU cc_start: 0.9122 (mp) cc_final: 0.8756 (tt) REVERT: A 454 MET cc_start: 0.9103 (tpp) cc_final: 0.8762 (tpp) REVERT: A 497 MET cc_start: 0.8263 (ttp) cc_final: 0.7912 (ttm) REVERT: A 515 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8158 (mm-30) REVERT: A 589 ARG cc_start: 0.7225 (mmt180) cc_final: 0.6918 (mmt180) REVERT: A 602 VAL cc_start: 0.9360 (t) cc_final: 0.9047 (p) REVERT: A 607 LYS cc_start: 0.8467 (mttp) cc_final: 0.8130 (mtmt) REVERT: A 629 TRP cc_start: 0.7567 (m-10) cc_final: 0.7295 (m-10) REVERT: B 35 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8527 (mp0) REVERT: B 78 MET cc_start: 0.7994 (ptp) cc_final: 0.7716 (ptp) REVERT: B 96 MET cc_start: 0.8513 (mmm) cc_final: 0.7948 (mmm) REVERT: B 363 ARG cc_start: 0.7730 (mmm160) cc_final: 0.7250 (mmm160) REVERT: B 497 MET cc_start: 0.7916 (ttp) cc_final: 0.7332 (ttm) REVERT: B 570 MET cc_start: 0.8334 (ttm) cc_final: 0.7686 (tpp) REVERT: B 602 VAL cc_start: 0.9401 (t) cc_final: 0.9098 (p) REVERT: B 607 LYS cc_start: 0.8646 (mttp) cc_final: 0.8347 (mtmt) REVERT: C 35 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8609 (mp0) REVERT: C 61 LEU cc_start: 0.8687 (mt) cc_final: 0.8467 (mt) REVERT: C 96 MET cc_start: 0.8696 (mmm) cc_final: 0.8308 (mmm) REVERT: C 130 MET cc_start: 0.8205 (tpt) cc_final: 0.7457 (tpp) REVERT: C 305 ARG cc_start: 0.8699 (mmt180) cc_final: 0.8350 (mmt-90) REVERT: C 363 ARG cc_start: 0.7716 (mmm160) cc_final: 0.7450 (mmm160) REVERT: C 386 LEU cc_start: 0.9264 (tp) cc_final: 0.8995 (pp) REVERT: C 454 MET cc_start: 0.9255 (tpt) cc_final: 0.8987 (tpp) REVERT: C 472 PHE cc_start: 0.6899 (t80) cc_final: 0.6590 (t80) REVERT: C 495 TRP cc_start: 0.8403 (t-100) cc_final: 0.8047 (t-100) REVERT: C 497 MET cc_start: 0.8037 (ttp) cc_final: 0.7753 (ttm) REVERT: C 539 THR cc_start: 0.9203 (m) cc_final: 0.8942 (p) REVERT: C 593 TRP cc_start: 0.8744 (t60) cc_final: 0.8338 (t60) REVERT: C 602 VAL cc_start: 0.9419 (t) cc_final: 0.9178 (p) REVERT: C 607 LYS cc_start: 0.8621 (mttp) cc_final: 0.8219 (mtmt) REVERT: D 35 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8558 (mp0) REVERT: D 38 LEU cc_start: 0.8445 (tp) cc_final: 0.8121 (tp) REVERT: D 61 LEU cc_start: 0.8730 (mt) cc_final: 0.8523 (mt) REVERT: D 96 MET cc_start: 0.8644 (mmm) cc_final: 0.8113 (mmm) REVERT: D 113 GLU cc_start: 0.7950 (mp0) cc_final: 0.7708 (mp0) REVERT: D 116 GLU cc_start: 0.7632 (mp0) cc_final: 0.7291 (mp0) REVERT: D 130 MET cc_start: 0.8216 (tpt) cc_final: 0.7710 (tpp) REVERT: D 339 TYR cc_start: 0.8626 (t80) cc_final: 0.8318 (t80) REVERT: D 454 MET cc_start: 0.9076 (tpp) cc_final: 0.8768 (tpp) REVERT: D 466 MET cc_start: 0.8321 (ttm) cc_final: 0.7812 (tmm) REVERT: D 497 MET cc_start: 0.8058 (ttp) cc_final: 0.7589 (ttm) REVERT: D 515 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7605 (tp30) REVERT: D 577 MET cc_start: 0.8574 (ttm) cc_final: 0.7952 (ttm) REVERT: D 593 TRP cc_start: 0.8927 (t60) cc_final: 0.8433 (t60) REVERT: D 602 VAL cc_start: 0.9373 (t) cc_final: 0.9042 (p) REVERT: D 607 LYS cc_start: 0.8547 (mttp) cc_final: 0.8221 (mtmt) outliers start: 4 outliers final: 0 residues processed: 508 average time/residue: 0.2799 time to fit residues: 223.5110 Evaluate side-chains 418 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN B 174 ASN C 174 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19476 Z= 0.196 Angle : 0.717 15.460 26432 Z= 0.341 Chirality : 0.042 0.191 3012 Planarity : 0.004 0.043 3336 Dihedral : 4.641 29.128 2592 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.19 % Allowed : 0.82 % Favored : 98.98 % 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: -0.62 (0.18), residues: 2356 helix: 1.00 (0.15), residues: 1276 sheet: -2.38 (0.57), residues: 76 loop : -2.20 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 583 HIS 0.002 0.000 HIS D 122 PHE 0.023 0.001 PHE B 434 TYR 0.013 0.001 TYR D 524 ARG 0.005 0.000 ARG B 610 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 498 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8588 (mp0) REVERT: A 38 LEU cc_start: 0.8464 (tp) cc_final: 0.8106 (tp) REVERT: A 55 ASP cc_start: 0.8509 (t70) cc_final: 0.7872 (t70) REVERT: A 61 LEU cc_start: 0.8712 (mt) cc_final: 0.8211 (mt) REVERT: A 96 MET cc_start: 0.8664 (mmm) cc_final: 0.8328 (mmm) REVERT: A 130 MET cc_start: 0.8086 (tpt) cc_final: 0.7443 (tpp) REVERT: A 217 ASN cc_start: 0.8919 (t0) cc_final: 0.8660 (t0) REVERT: A 363 ARG cc_start: 0.8666 (mtt180) cc_final: 0.8364 (ptm160) REVERT: A 434 PHE cc_start: 0.8299 (t80) cc_final: 0.7986 (t80) REVERT: A 437 LEU cc_start: 0.9089 (mp) cc_final: 0.8699 (tt) REVERT: A 454 MET cc_start: 0.9085 (tpp) cc_final: 0.8774 (tpp) REVERT: A 497 MET cc_start: 0.8325 (ttp) cc_final: 0.7958 (ttm) REVERT: A 515 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8190 (mm-30) REVERT: A 589 ARG cc_start: 0.7228 (mmt180) cc_final: 0.6908 (mmt180) REVERT: A 602 VAL cc_start: 0.9311 (t) cc_final: 0.8991 (p) REVERT: A 607 LYS cc_start: 0.8483 (mttp) cc_final: 0.8133 (mtmt) REVERT: A 629 TRP cc_start: 0.7707 (m-10) cc_final: 0.7408 (m-10) REVERT: B 35 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8560 (mp0) REVERT: B 96 MET cc_start: 0.8528 (mmm) cc_final: 0.7932 (mmm) REVERT: B 363 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7245 (mmm160) REVERT: B 497 MET cc_start: 0.7927 (ttp) cc_final: 0.7435 (ttm) REVERT: B 570 MET cc_start: 0.8192 (ttm) cc_final: 0.7609 (tpp) REVERT: B 589 ARG cc_start: 0.7835 (tpp-160) cc_final: 0.7527 (mmt180) REVERT: B 602 VAL cc_start: 0.9458 (t) cc_final: 0.9178 (p) REVERT: B 607 LYS cc_start: 0.8656 (mttp) cc_final: 0.8333 (mtmt) REVERT: C 35 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8630 (mp0) REVERT: C 40 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8762 (tm-30) REVERT: C 61 LEU cc_start: 0.8903 (mt) cc_final: 0.8283 (mt) REVERT: C 75 ARG cc_start: 0.7935 (mmt90) cc_final: 0.7649 (mmt90) REVERT: C 96 MET cc_start: 0.8694 (mmm) cc_final: 0.8305 (mmm) REVERT: C 130 MET cc_start: 0.8135 (tpt) cc_final: 0.7659 (tpp) REVERT: C 305 ARG cc_start: 0.8703 (mmt180) cc_final: 0.8360 (mmt-90) REVERT: C 363 ARG cc_start: 0.7734 (mmm160) cc_final: 0.6952 (mmm160) REVERT: C 386 LEU cc_start: 0.9288 (tp) cc_final: 0.9015 (pp) REVERT: C 472 PHE cc_start: 0.6928 (t80) cc_final: 0.6605 (t80) REVERT: C 497 MET cc_start: 0.8109 (ttp) cc_final: 0.7815 (ttm) REVERT: C 539 THR cc_start: 0.9220 (m) cc_final: 0.8998 (p) REVERT: C 593 TRP cc_start: 0.8813 (t60) cc_final: 0.8332 (t60) REVERT: C 602 VAL cc_start: 0.9443 (t) cc_final: 0.9216 (p) REVERT: C 607 LYS cc_start: 0.8584 (mttp) cc_final: 0.8160 (mtmt) REVERT: D 35 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8587 (mp0) REVERT: D 38 LEU cc_start: 0.8479 (tp) cc_final: 0.8170 (tp) REVERT: D 61 LEU cc_start: 0.8932 (mt) cc_final: 0.8298 (mt) REVERT: D 96 MET cc_start: 0.8695 (mmm) cc_final: 0.8164 (mmm) REVERT: D 113 GLU cc_start: 0.8066 (mp0) cc_final: 0.7771 (mp0) REVERT: D 116 GLU cc_start: 0.7720 (mp0) cc_final: 0.7226 (mp0) REVERT: D 130 MET cc_start: 0.8230 (tpt) cc_final: 0.7716 (tpp) REVERT: D 339 TYR cc_start: 0.8579 (t80) cc_final: 0.8289 (t80) REVERT: D 454 MET cc_start: 0.9083 (tpp) cc_final: 0.8766 (tpp) REVERT: D 466 MET cc_start: 0.8275 (ttm) cc_final: 0.7794 (tmm) REVERT: D 497 MET cc_start: 0.8097 (ttp) cc_final: 0.7660 (ttm) REVERT: D 515 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7605 (tp30) REVERT: D 577 MET cc_start: 0.8562 (ttm) cc_final: 0.7951 (ttm) REVERT: D 593 TRP cc_start: 0.8914 (t60) cc_final: 0.8420 (t60) REVERT: D 602 VAL cc_start: 0.9386 (t) cc_final: 0.9077 (p) REVERT: D 607 LYS cc_start: 0.8477 (mttp) cc_final: 0.8147 (mtmt) outliers start: 4 outliers final: 0 residues processed: 502 average time/residue: 0.2829 time to fit residues: 221.5122 Evaluate side-chains 418 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.0010 chunk 106 optimal weight: 0.0970 chunk 155 optimal weight: 0.0770 chunk 235 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 chunk 187 optimal weight: 0.0040 chunk 19 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 overall best weight: 0.1554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN B 174 ASN C 174 ASN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19476 Z= 0.152 Angle : 0.703 15.394 26432 Z= 0.330 Chirality : 0.041 0.171 3012 Planarity : 0.004 0.043 3336 Dihedral : 4.539 29.250 2592 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.19 % Allowed : 0.24 % Favored : 99.56 % 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: -0.50 (0.18), residues: 2356 helix: 1.13 (0.15), residues: 1252 sheet: -2.25 (0.56), residues: 76 loop : -2.12 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 583 HIS 0.002 0.000 HIS A 522 PHE 0.029 0.001 PHE C 434 TYR 0.011 0.001 TYR D 524 ARG 0.004 0.000 ARG C 610 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 537 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8499 (mp0) REVERT: A 61 LEU cc_start: 0.8655 (mt) cc_final: 0.8178 (mt) REVERT: A 92 LEU cc_start: 0.8589 (pt) cc_final: 0.7949 (pt) REVERT: A 96 MET cc_start: 0.8483 (mmm) cc_final: 0.7924 (mmm) REVERT: A 130 MET cc_start: 0.7903 (tpt) cc_final: 0.7415 (tpp) REVERT: A 211 PHE cc_start: 0.7988 (t80) cc_final: 0.7639 (t80) REVERT: A 216 TYR cc_start: 0.8932 (t80) cc_final: 0.8731 (t80) REVERT: A 279 ASP cc_start: 0.8490 (t70) cc_final: 0.8189 (t70) REVERT: A 454 MET cc_start: 0.9121 (tpp) cc_final: 0.8867 (tpp) REVERT: A 485 MET cc_start: 0.6756 (pmm) cc_final: 0.5927 (pmm) REVERT: A 515 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8070 (mm-30) REVERT: A 573 LEU cc_start: 0.9297 (tp) cc_final: 0.9078 (tp) REVERT: A 602 VAL cc_start: 0.9350 (t) cc_final: 0.9086 (p) REVERT: A 607 LYS cc_start: 0.8405 (mttp) cc_final: 0.8054 (mtmt) REVERT: A 629 TRP cc_start: 0.7499 (m-10) cc_final: 0.7235 (m-10) REVERT: B 35 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8495 (mp0) REVERT: B 55 ASP cc_start: 0.8567 (t70) cc_final: 0.8024 (t70) REVERT: B 92 LEU cc_start: 0.8538 (tp) cc_final: 0.8310 (tp) REVERT: B 96 MET cc_start: 0.8411 (mmm) cc_final: 0.7822 (mmm) REVERT: B 130 MET cc_start: 0.7944 (tpt) cc_final: 0.7442 (tpp) REVERT: B 363 ARG cc_start: 0.7629 (mmm160) cc_final: 0.7384 (mmm160) REVERT: B 495 TRP cc_start: 0.8178 (t-100) cc_final: 0.7945 (t-100) REVERT: B 497 MET cc_start: 0.7857 (ttp) cc_final: 0.7412 (ttm) REVERT: B 570 MET cc_start: 0.8226 (ttm) cc_final: 0.7660 (tpp) REVERT: B 602 VAL cc_start: 0.9438 (t) cc_final: 0.9123 (p) REVERT: B 607 LYS cc_start: 0.8616 (mttp) cc_final: 0.8252 (mtmt) REVERT: C 35 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8593 (mp0) REVERT: C 61 LEU cc_start: 0.8678 (mt) cc_final: 0.8241 (mt) REVERT: C 92 LEU cc_start: 0.8711 (pt) cc_final: 0.8186 (pt) REVERT: C 96 MET cc_start: 0.8607 (mmm) cc_final: 0.8049 (mmm) REVERT: C 113 GLU cc_start: 0.7426 (mp0) cc_final: 0.7199 (mp0) REVERT: C 130 MET cc_start: 0.7907 (tpt) cc_final: 0.7503 (tpp) REVERT: C 363 ARG cc_start: 0.7660 (mmm160) cc_final: 0.7387 (mmm160) REVERT: C 383 ASP cc_start: 0.8699 (m-30) cc_final: 0.8357 (t70) REVERT: C 386 LEU cc_start: 0.9265 (tp) cc_final: 0.9032 (pp) REVERT: C 472 PHE cc_start: 0.6840 (t80) cc_final: 0.6640 (t80) REVERT: C 495 TRP cc_start: 0.8241 (t-100) cc_final: 0.7960 (t-100) REVERT: C 497 MET cc_start: 0.8030 (ttp) cc_final: 0.7817 (ttm) REVERT: C 539 THR cc_start: 0.9048 (m) cc_final: 0.8782 (p) REVERT: C 570 MET cc_start: 0.8198 (ttm) cc_final: 0.7751 (tpp) REVERT: C 593 TRP cc_start: 0.8702 (t60) cc_final: 0.8291 (t60) REVERT: C 607 LYS cc_start: 0.8489 (mttp) cc_final: 0.8122 (mtmt) REVERT: C 610 ARG cc_start: 0.8686 (tpp80) cc_final: 0.7996 (mmm160) REVERT: D 35 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8532 (mp0) REVERT: D 38 LEU cc_start: 0.8432 (tp) cc_final: 0.8117 (tp) REVERT: D 61 LEU cc_start: 0.8715 (mt) cc_final: 0.8298 (mt) REVERT: D 92 LEU cc_start: 0.8655 (tp) cc_final: 0.8405 (tp) REVERT: D 96 MET cc_start: 0.8585 (mmm) cc_final: 0.8026 (mmm) REVERT: D 113 GLU cc_start: 0.7780 (mp0) cc_final: 0.7541 (mp0) REVERT: D 116 GLU cc_start: 0.7352 (mp0) cc_final: 0.7062 (mp0) REVERT: D 130 MET cc_start: 0.8023 (tpt) cc_final: 0.7647 (tpp) REVERT: D 279 ASP cc_start: 0.8046 (t70) cc_final: 0.7729 (t70) REVERT: D 339 TYR cc_start: 0.8665 (t80) cc_final: 0.8346 (t80) REVERT: D 454 MET cc_start: 0.9202 (tpp) cc_final: 0.8956 (tpp) REVERT: D 466 MET cc_start: 0.8269 (ttm) cc_final: 0.7792 (tmm) REVERT: D 497 MET cc_start: 0.8245 (ttp) cc_final: 0.7835 (ttm) REVERT: D 515 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7557 (tp30) REVERT: D 593 TRP cc_start: 0.8817 (t60) cc_final: 0.8300 (t60) REVERT: D 602 VAL cc_start: 0.9360 (t) cc_final: 0.9108 (p) REVERT: D 607 LYS cc_start: 0.8399 (mttp) cc_final: 0.8105 (mtmt) outliers start: 4 outliers final: 0 residues processed: 541 average time/residue: 0.2834 time to fit residues: 237.9092 Evaluate side-chains 431 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 174 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 174 ASN C 165 HIS C 174 ASN D 174 ASN D 252 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.089241 restraints weight = 45750.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.091600 restraints weight = 28354.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.093189 restraints weight = 20666.243| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 19476 Z= 0.317 Angle : 0.794 15.803 26432 Z= 0.387 Chirality : 0.046 0.183 3012 Planarity : 0.005 0.079 3336 Dihedral : 4.780 29.191 2592 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 0.19 % Allowed : 0.48 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.65 (0.18), residues: 2356 helix: 0.98 (0.15), residues: 1272 sheet: -2.20 (0.61), residues: 76 loop : -2.22 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 583 HIS 0.004 0.001 HIS D 122 PHE 0.019 0.002 PHE C 434 TYR 0.020 0.002 TYR C 467 ARG 0.018 0.001 ARG C 492 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4639.91 seconds wall clock time: 84 minutes 25.51 seconds (5065.51 seconds total)