Starting phenix.real_space_refine (version: dev) on Thu Feb 23 01:51:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6boa_7122/02_2023/6boa_7122.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6boa_7122/02_2023/6boa_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_2023/6boa_7122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6boa_7122/02_2023/6boa_7122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6boa_7122/02_2023/6boa_7122.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6boa_7122/02_2023/6boa_7122.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 10.78, per 1000 atoms: 0.57 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: 7.09 Conformation dependent library (CDL) restraints added in 2.9 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: 0.82 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: 5.15 Time building geometry restraints manager: 7.68 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 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. 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: 0.400 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: 0.010 Extract box with map and model: 3.610 Check model and map are aligned: 0.250 Process input model: 46.490 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 % 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 *********************** 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 : 2.309 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 outliers start: 36 outliers final: 10 residues processed: 762 average time/residue: 0.3057 time to fit residues: 351.0398 Evaluate side-chains 432 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 422 time to evaluate : 2.508 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1684 time to fit residues: 6.2775 ------------------------------------------------------------------------------- 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: 0.8980 chunk 178 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 184 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3767 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= 0.225 Angle : 0.794 14.299 26432 Z= 0.399 Chirality : 0.044 0.185 3012 Planarity : 0.005 0.042 3336 Dihedral : 6.246 30.599 2592 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.31 % Favored : 89.64 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.04 % 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: -3.60 (0.15), residues: 2356 helix: -1.86 (0.12), residues: 1356 sheet: -4.45 (0.32), residues: 76 loop : -2.88 (0.19), residues: 924 *********************** 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 577 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 566 time to evaluate : 2.271 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 outliers start: 11 outliers final: 1 residues processed: 568 average time/residue: 0.2893 time to fit residues: 252.6356 Evaluate side-chains 415 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 414 time to evaluate : 2.351 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1687 time to fit residues: 3.5598 ------------------------------------------------------------------------------- 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: 5.9990 chunk 66 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 B 91 ASN B 257 GLN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 19476 Z= 0.260 Angle : 0.772 14.315 26432 Z= 0.384 Chirality : 0.044 0.168 3012 Planarity : 0.004 0.044 3336 Dihedral : 5.599 30.345 2592 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer Outliers : 0.29 % 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: -2.46 (0.16), residues: 2356 helix: -0.66 (0.14), residues: 1332 sheet: -4.03 (0.38), residues: 76 loop : -2.82 (0.19), residues: 948 *********************** 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 486 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 480 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 482 average time/residue: 0.3017 time to fit residues: 222.0107 Evaluate side-chains 395 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 2.363 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2995 ------------------------------------------------------------------------------- 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: 0.8980 chunk 161 optimal weight: 10.0000 chunk 111 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- 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 ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 174 ASN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN D 464 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4931 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= 0.188 Angle : 0.711 14.324 26432 Z= 0.347 Chirality : 0.042 0.177 3012 Planarity : 0.004 0.044 3336 Dihedral : 5.198 30.357 2592 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer Outliers : 0.05 % 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: -1.43 (0.18), residues: 2356 helix: 0.15 (0.15), residues: 1260 sheet: -3.64 (0.42), residues: 76 loop : -2.16 (0.20), residues: 1020 *********************** 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 515 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 514 time to evaluate : 2.086 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 outliers start: 1 outliers final: 0 residues processed: 515 average time/residue: 0.2861 time to fit residues: 228.8403 Evaluate side-chains 419 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 2.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3305 ------------------------------------------------------------------------------- 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: 5.9990 chunk 129 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 204 optimal weight: 0.0020 chunk 57 optimal weight: 10.0000 overall best weight: 3.5594 ------------------------------------------------------------------------------- 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 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN 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 174 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8235 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 19476 Z= 0.345 Angle : 0.808 15.266 26432 Z= 0.398 Chirality : 0.046 0.243 3012 Planarity : 0.005 0.048 3336 Dihedral : 5.313 29.599 2592 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.27 % Favored : 89.69 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2356 helix: 0.21 (0.14), residues: 1284 sheet: -3.42 (0.48), residues: 76 loop : -2.42 (0.20), residues: 996 *********************** 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 471 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 468 time to evaluate : 2.236 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 outliers start: 3 outliers final: 0 residues processed: 471 average time/residue: 0.2917 time to fit residues: 212.7165 Evaluate side-chains 381 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 2.088 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8508 ------------------------------------------------------------------------------- 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: 0.7980 chunk 205 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 189 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 62 ASN C 174 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 206 GLN D 357 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5529 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= 0.175 Angle : 0.723 13.959 26432 Z= 0.350 Chirality : 0.042 0.169 3012 Planarity : 0.004 0.046 3336 Dihedral : 5.010 30.806 2592 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.00 % 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: -1.00 (0.18), residues: 2356 helix: 0.61 (0.15), residues: 1288 sheet: -3.00 (0.50), residues: 76 loop : -2.23 (0.21), residues: 992 *********************** 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 504 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 502 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 504 average time/residue: 0.2922 time to fit residues: 228.7816 Evaluate side-chains 400 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 2.223 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0581 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 0.0670 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 192 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 138 optimal weight: 0.0020 chunk 105 optimal weight: 4.9990 overall best weight: 0.9530 ------------------------------------------------------------------------------- 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 B 118 GLN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8131 moved from start: 0.5788 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= 0.178 Angle : 0.715 15.094 26432 Z= 0.346 Chirality : 0.042 0.172 3012 Planarity : 0.004 0.045 3336 Dihedral : 4.884 30.032 2592 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.85 % Favored : 90.11 % Rotamer Outliers : 0.15 % 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: -0.80 (0.18), residues: 2356 helix: 0.78 (0.15), residues: 1252 sheet: -2.78 (0.52), residues: 76 loop : -2.07 (0.20), residues: 1028 *********************** 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 488 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 485 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 488 average time/residue: 0.2839 time to fit residues: 217.1492 Evaluate side-chains 393 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.245 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0813 ------------------------------------------------------------------------------- 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: 6.9990 chunk 90 optimal weight: 0.0870 chunk 135 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 144 optimal weight: 0.0040 chunk 154 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 overall best weight: 0.6174 ------------------------------------------------------------------------------- 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 B 118 GLN B 174 ASN B 464 ASN C 174 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 174 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: 0.8096 moved from start: 0.5986 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= 0.164 Angle : 0.706 15.350 26432 Z= 0.338 Chirality : 0.042 0.168 3012 Planarity : 0.004 0.045 3336 Dihedral : 4.759 32.285 2592 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -0.66 (0.18), residues: 2356 helix: 0.91 (0.15), residues: 1244 sheet: -2.58 (0.53), residues: 76 loop : -2.01 (0.21), residues: 1036 *********************** 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 500 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 496 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 500 average time/residue: 0.2852 time to fit residues: 222.9954 Evaluate side-chains 402 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 2.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0067 ------------------------------------------------------------------------------- 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: 0.0770 chunk 198 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 127 optimal weight: 0.2980 chunk 92 optimal weight: 8.9990 chunk 166 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 B 464 ASN C 174 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 174 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19476 Z= 0.174 Angle : 0.718 15.331 26432 Z= 0.343 Chirality : 0.042 0.202 3012 Planarity : 0.004 0.044 3336 Dihedral : 4.689 29.515 2592 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 0.19 % 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: 1.04 (0.15), residues: 1236 sheet: -2.46 (0.55), residues: 76 loop : -1.92 (0.21), residues: 1044 *********************** 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 491 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 487 time to evaluate : 2.298 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 outliers start: 4 outliers final: 0 residues processed: 491 average time/residue: 0.2807 time to fit residues: 216.3623 Evaluate side-chains 400 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 2.276 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9850 ------------------------------------------------------------------------------- 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: 5.9990 chunk 106 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8128 moved from start: 0.6178 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= 0.205 Angle : 0.736 15.578 26432 Z= 0.358 Chirality : 0.043 0.198 3012 Planarity : 0.004 0.044 3336 Dihedral : 4.741 30.741 2592 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer Outliers : 0.19 % 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: -0.50 (0.18), residues: 2356 helix: 1.07 (0.15), residues: 1232 sheet: -2.43 (0.57), residues: 76 loop : -1.96 (0.20), residues: 1048 ********************** 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 482 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 478 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 482 average time/residue: 0.2868 time to fit residues: 218.6495 Evaluate side-chains 397 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 2.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1612 ------------------------------------------------------------------------------- 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: 0.9990 chunk 172 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN B 165 HIS B 174 ASN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 174 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 165 HIS D 174 ASN D 252 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.090468 restraints weight = 46369.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.092863 restraints weight = 28097.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.094492 restraints weight = 20382.133| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 19476 Z= 0.263 Angle : 0.789 15.752 26432 Z= 0.382 Chirality : 0.045 0.206 3012 Planarity : 0.004 0.044 3336 Dihedral : 4.880 29.990 2592 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer Outliers : 0.19 % 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: -0.72 (0.18), residues: 2356 helix: 0.92 (0.15), residues: 1268 sheet: -2.35 (0.59), residues: 76 loop : -2.23 (0.20), residues: 1012 =============================================================================== Job complete usr+sys time: 4267.59 seconds wall clock time: 77 minutes 36.55 seconds (4656.55 seconds total)