Starting phenix.real_space_refine on Tue Apr 9 15:47:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm0_17755/04_2024/8pm0_17755_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm0_17755/04_2024/8pm0_17755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm0_17755/04_2024/8pm0_17755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm0_17755/04_2024/8pm0_17755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm0_17755/04_2024/8pm0_17755_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm0_17755/04_2024/8pm0_17755_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 141 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 33 5.49 5 Mg 1 5.21 5 S 120 5.16 5 C 10367 2.51 5 N 2906 2.21 5 O 3242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B GLU 656": "OE1" <-> "OE2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 492": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16669 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5748 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 5850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5850 Classifications: {'peptide': 735} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4283 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 19, 'TRANS': 517} Chain: "V" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 659 Classifications: {'RNA': 31} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 13} Link IDs: {'rna2p': 7, 'rna3p': 23} Chain breaks: 1 Chain: "P" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 73 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 2, 'TRANS': 6} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 2, 'TRANS': 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.22, per 1000 atoms: 0.55 Number of scatterers: 16669 At special positions: 0 Unit cell: (96.6, 122.64, 145.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 33 15.00 Mg 1 11.99 O 3242 8.00 N 2906 7.00 C 10367 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: 6.57 Conformation dependent library (CDL) restraints added in 2.6 seconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 20 sheets defined 43.7% alpha, 11.9% beta 6 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 7.43 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.812A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 165 through 185 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.754A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 434 through 451 Processing helix chain 'A' and resid 454 through 475 Processing helix chain 'A' and resid 530 through 537 Proline residue: A 534 - end of helix Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 581 through 600 removed outlier: 3.719A pdb=" N SER A 594 " --> pdb=" O GLN A 591 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 597 " --> pdb=" O SER A 594 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 598 " --> pdb=" O MET A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 633 through 649 Processing helix chain 'A' and resid 653 through 673 removed outlier: 4.043A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 3.976A pdb=" N CYS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 714 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 15 through 21 removed outlier: 5.849A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 160 removed outlier: 3.899A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 160' Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.693A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 249 through 265 removed outlier: 3.786A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 290 Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 345 removed outlier: 4.537A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 383 through 395 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.738A pdb=" N THR B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 506 through 511 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 519 through 536 Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 591 through 593 No H-bonds generated for 'chain 'B' and resid 591 through 593' Processing helix chain 'B' and resid 608 through 611 No H-bonds generated for 'chain 'B' and resid 608 through 611' Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 673 through 676 Processing helix chain 'B' and resid 678 through 699 removed outlier: 4.157A pdb=" N GLY B 681 " --> pdb=" O SER B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 3.791A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 714 through 731 Processing helix chain 'B' and resid 737 through 755 removed outlier: 3.833A pdb=" N ARG B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 25 through 31 removed outlier: 4.019A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 111 through 114 No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 116 through 127 Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 180 through 192 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 229 through 235 removed outlier: 5.386A pdb=" N HIS C 233 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 272 removed outlier: 3.861A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 286 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.651A pdb=" N MET C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 405 Processing helix chain 'C' and resid 408 through 411 No H-bonds generated for 'chain 'C' and resid 408 through 411' Processing helix chain 'C' and resid 430 through 440 Processing helix chain 'C' and resid 443 through 449 Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing sheet with id= A, first strand: chain 'A' and resid 76 through 78 Processing sheet with id= B, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.670A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.709A pdb=" N GLY A 546 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N THR A 567 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR A 540 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 619 through 624 removed outlier: 6.910A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= F, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= G, first strand: chain 'B' and resid 178 through 183 Processing sheet with id= H, first strand: chain 'B' and resid 224 through 228 Processing sheet with id= I, first strand: chain 'B' and resid 484 through 486 Processing sheet with id= J, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= K, first strand: chain 'B' and resid 354 through 359 Processing sheet with id= L, first strand: chain 'B' and resid 489 through 492 Processing sheet with id= M, first strand: chain 'B' and resid 642 through 645 Processing sheet with id= N, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= O, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= P, first strand: chain 'C' and resid 141 through 145 Processing sheet with id= Q, first strand: chain 'C' and resid 287 through 289 Processing sheet with id= R, first strand: chain 'C' and resid 323 through 325 removed outlier: 6.745A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ALA C 377 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 338 through 345 Processing sheet with id= T, first strand: chain 'C' and resid 496 through 498 675 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 5.92 Time building geometry restraints manager: 7.05 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: 5352 1.34 - 1.46: 2954 1.46 - 1.58: 8471 1.58 - 1.70: 68 1.70 - 1.82: 208 Bond restraints: 17053 Sorted by residual: bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" CB GLU B 267 " pdb=" CG GLU B 267 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" C LYS B 353 " pdb=" N GLY B 354 " ideal model delta sigma weight residual 1.335 1.328 0.007 7.50e-03 1.78e+04 8.80e-01 bond pdb=" CA GLY B 354 " pdb=" C GLY B 354 " ideal model delta sigma weight residual 1.522 1.511 0.011 1.30e-02 5.92e+03 7.60e-01 ... (remaining 17048 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.87: 643 106.87 - 113.66: 9430 113.66 - 120.45: 6489 120.45 - 127.23: 6358 127.23 - 134.02: 227 Bond angle restraints: 23147 Sorted by residual: angle pdb=" N ILE A 323 " pdb=" CA ILE A 323 " pdb=" C ILE A 323 " ideal model delta sigma weight residual 111.56 108.63 2.93 8.60e-01 1.35e+00 1.16e+01 angle pdb=" CB MET B 407 " pdb=" CG MET B 407 " pdb=" SD MET B 407 " ideal model delta sigma weight residual 112.70 120.80 -8.10 3.00e+00 1.11e-01 7.30e+00 angle pdb=" N ILE B 248 " pdb=" CA ILE B 248 " pdb=" C ILE B 248 " ideal model delta sigma weight residual 113.20 110.89 2.31 9.60e-01 1.09e+00 5.77e+00 angle pdb=" CA GLY B 500 " pdb=" C GLY B 500 " pdb=" N PHE B 501 " ideal model delta sigma weight residual 115.62 117.36 -1.74 7.60e-01 1.73e+00 5.25e+00 angle pdb=" CB GLU B 267 " pdb=" CG GLU B 267 " pdb=" CD GLU B 267 " ideal model delta sigma weight residual 112.60 116.46 -3.86 1.70e+00 3.46e-01 5.15e+00 ... (remaining 23142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8851 17.82 - 35.65: 1110 35.65 - 53.47: 382 53.47 - 71.29: 123 71.29 - 89.11: 41 Dihedral angle restraints: 10507 sinusoidal: 4690 harmonic: 5817 Sorted by residual: dihedral pdb=" CB GLU A 457 " pdb=" CG GLU A 457 " pdb=" CD GLU A 457 " pdb=" OE1 GLU A 457 " ideal model delta sinusoidal sigma weight residual 0.00 89.11 -89.11 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 56 " pdb=" CG GLU A 56 " pdb=" CD GLU A 56 " pdb=" OE1 GLU A 56 " ideal model delta sinusoidal sigma weight residual 0.00 -88.18 88.18 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU B 78 " pdb=" CG GLU B 78 " pdb=" CD GLU B 78 " pdb=" OE1 GLU B 78 " ideal model delta sinusoidal sigma weight residual 0.00 -87.11 87.11 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 10504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1625 0.028 - 0.057: 681 0.057 - 0.085: 138 0.085 - 0.114: 95 0.114 - 0.142: 35 Chirality restraints: 2574 Sorted by residual: chirality pdb=" CA ILE C 385 " pdb=" N ILE C 385 " pdb=" C ILE C 385 " pdb=" CB ILE C 385 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE B 450 " pdb=" N ILE B 450 " pdb=" C ILE B 450 " pdb=" CB ILE B 450 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA ILE B 667 " pdb=" N ILE B 667 " pdb=" C ILE B 667 " pdb=" CB ILE B 667 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 2571 not shown) Planarity restraints: 2870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.028 2.00e-02 2.50e+03 1.26e-02 4.37e+00 pdb=" N9 A V 4 " 0.029 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 514 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO C 515 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 515 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 515 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 587 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C GLN A 587 " -0.027 2.00e-02 2.50e+03 pdb=" O GLN A 587 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 588 " 0.009 2.00e-02 2.50e+03 ... (remaining 2867 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 155 2.58 - 3.16: 13941 3.16 - 3.74: 26636 3.74 - 4.32: 37928 4.32 - 4.90: 62359 Nonbonded interactions: 141019 Sorted by model distance: nonbonded pdb=" O PHE B 700 " pdb=" OG SER B 703 " model vdw 1.995 2.440 nonbonded pdb=" O ARG B 334 " pdb=" OG SER B 338 " model vdw 2.044 2.440 nonbonded pdb=" O MET C 11 " pdb=" NH1 ARG C 17 " model vdw 2.053 2.520 nonbonded pdb=" OG SER B 19 " pdb=" OG SER B 506 " model vdw 2.066 2.440 nonbonded pdb=" O MET B 409 " pdb=" N2 G V 49 " model vdw 2.085 2.520 ... (remaining 141014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 10.070 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 49.650 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 : 0.003 0.033 17053 Z= 0.174 Angle : 0.475 8.104 23147 Z= 0.251 Chirality : 0.037 0.142 2574 Planarity : 0.003 0.046 2870 Dihedral : 19.028 89.113 6737 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.14 % Allowed : 25.54 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.93 (0.19), residues: 1976 helix: 1.73 (0.18), residues: 885 sheet: 0.04 (0.33), residues: 237 loop : -0.35 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 438 HIS 0.002 0.001 HIS C 151 PHE 0.010 0.001 PHE C 119 TYR 0.013 0.001 TYR B 555 ARG 0.002 0.000 ARG C 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 1.949 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.2632 (tmt) cc_final: 0.2256 (ptm) REVERT: B 227 MET cc_start: 0.8830 (pmm) cc_final: 0.8332 (pmm) REVERT: C 536 MET cc_start: 0.4509 (mmm) cc_final: 0.4292 (mmm) outliers start: 38 outliers final: 30 residues processed: 208 average time/residue: 1.4000 time to fit residues: 324.4800 Evaluate side-chains 196 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 455 ASP Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 530 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 155 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS B 184 HIS B 687 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17053 Z= 0.167 Angle : 0.475 6.781 23147 Z= 0.248 Chirality : 0.039 0.154 2574 Planarity : 0.004 0.048 2870 Dihedral : 10.817 73.788 2707 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.65 % Allowed : 24.35 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.86 (0.19), residues: 1976 helix: 1.59 (0.18), residues: 899 sheet: 0.22 (0.33), residues: 226 loop : -0.39 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.008 0.001 HIS B 649 PHE 0.009 0.001 PHE A 520 TYR 0.014 0.001 TYR B 555 ARG 0.007 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 188 time to evaluate : 1.936 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.2972 (tmt) cc_final: 0.2469 (ptm) REVERT: B 227 MET cc_start: 0.8854 (pmm) cc_final: 0.8545 (pmm) REVERT: B 425 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8700 (t0) REVERT: B 656 GLU cc_start: 0.7180 (tt0) cc_final: 0.6931 (mm-30) REVERT: B 706 ARG cc_start: 0.7818 (ptp90) cc_final: 0.7483 (ptp90) REVERT: C 28 MET cc_start: 0.8237 (ttp) cc_final: 0.8033 (ttp) REVERT: C 146 ASP cc_start: 0.5838 (p0) cc_final: 0.5333 (p0) REVERT: C 368 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6297 (mtp-110) outliers start: 47 outliers final: 17 residues processed: 221 average time/residue: 1.4252 time to fit residues: 348.4003 Evaluate side-chains 196 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 483 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 150 optimal weight: 0.2980 chunk 123 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 chunk 195 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 GLN B 105 ASN B 184 HIS B 562 HIS ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17053 Z= 0.171 Angle : 0.459 6.867 23147 Z= 0.240 Chirality : 0.039 0.152 2574 Planarity : 0.004 0.052 2870 Dihedral : 10.487 73.552 2677 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.93 % Allowed : 25.37 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 1976 helix: 1.57 (0.18), residues: 893 sheet: 0.23 (0.33), residues: 226 loop : -0.41 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.006 0.001 HIS C 151 PHE 0.010 0.001 PHE A 520 TYR 0.014 0.001 TYR B 555 ARG 0.002 0.000 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 182 time to evaluate : 1.915 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.2416 (tmt) cc_final: 0.2145 (ptm) REVERT: A 294 ASP cc_start: 0.7694 (t0) cc_final: 0.7299 (t0) REVERT: A 382 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: A 399 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: B 425 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8782 (t0) REVERT: B 656 GLU cc_start: 0.7196 (tt0) cc_final: 0.6948 (mm-30) REVERT: C 13 GLN cc_start: 0.6961 (tm-30) cc_final: 0.6456 (tm-30) REVERT: C 146 ASP cc_start: 0.5962 (p0) cc_final: 0.5403 (p0) REVERT: C 415 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6675 (mmt90) outliers start: 52 outliers final: 26 residues processed: 218 average time/residue: 1.5059 time to fit residues: 363.1286 Evaluate side-chains 199 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 483 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 192 optimal weight: 0.0170 chunk 94 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS B 649 HIS B 671 ASN B 687 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17053 Z= 0.158 Angle : 0.449 5.989 23147 Z= 0.235 Chirality : 0.038 0.149 2574 Planarity : 0.003 0.054 2870 Dihedral : 10.361 73.551 2674 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.93 % Allowed : 25.59 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 1976 helix: 1.60 (0.18), residues: 886 sheet: 0.22 (0.33), residues: 226 loop : -0.42 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.006 0.001 HIS C 151 PHE 0.010 0.001 PHE A 520 TYR 0.014 0.001 TYR B 555 ARG 0.003 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 185 time to evaluate : 1.885 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.2653 (tmt) cc_final: 0.2359 (ptp) REVERT: A 294 ASP cc_start: 0.7767 (t0) cc_final: 0.7351 (t0) REVERT: A 382 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: A 399 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7681 (pt0) REVERT: B 287 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7741 (mtt90) REVERT: B 656 GLU cc_start: 0.7190 (tt0) cc_final: 0.6948 (mm-30) REVERT: C 13 GLN cc_start: 0.6766 (tm-30) cc_final: 0.6372 (tm-30) REVERT: C 146 ASP cc_start: 0.6033 (p0) cc_final: 0.5409 (p0) REVERT: C 252 ASN cc_start: 0.6013 (OUTLIER) cc_final: 0.5777 (m110) REVERT: C 368 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6307 (mtp-110) outliers start: 52 outliers final: 23 residues processed: 220 average time/residue: 1.5002 time to fit residues: 364.2754 Evaluate side-chains 200 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 483 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 0.4980 chunk 172 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS B 184 HIS B 649 HIS B 687 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17053 Z= 0.366 Angle : 0.572 8.977 23147 Z= 0.296 Chirality : 0.043 0.205 2574 Planarity : 0.005 0.058 2870 Dihedral : 10.450 73.704 2669 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.06 % Allowed : 24.97 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.31 (0.18), residues: 1976 helix: 1.11 (0.17), residues: 899 sheet: -0.06 (0.32), residues: 245 loop : -0.65 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 438 HIS 0.006 0.001 HIS C 151 PHE 0.014 0.002 PHE A 520 TYR 0.019 0.002 TYR B 555 ARG 0.005 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 174 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4450 (OUTLIER) cc_final: 0.3487 (mtp180) REVERT: A 294 ASP cc_start: 0.7773 (t0) cc_final: 0.7389 (t0) REVERT: A 382 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7681 (pt0) REVERT: A 399 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7699 (pt0) REVERT: B 108 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7987 (mp) REVERT: B 656 GLU cc_start: 0.7257 (tt0) cc_final: 0.6999 (mm-30) REVERT: C 13 GLN cc_start: 0.6871 (tm-30) cc_final: 0.6624 (tm-30) REVERT: C 146 ASP cc_start: 0.6168 (p0) cc_final: 0.5600 (p0) REVERT: C 252 ASN cc_start: 0.5927 (OUTLIER) cc_final: 0.5724 (m110) REVERT: C 368 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6292 (mtp-110) REVERT: C 431 MET cc_start: 0.7322 (mtt) cc_final: 0.6988 (mtt) outliers start: 72 outliers final: 30 residues processed: 227 average time/residue: 1.5214 time to fit residues: 379.9887 Evaluate side-chains 203 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 167 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 532 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 0.9980 chunk 173 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 184 HIS ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17053 Z= 0.158 Angle : 0.471 9.231 23147 Z= 0.244 Chirality : 0.039 0.169 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.299 73.619 2669 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.71 % Allowed : 26.10 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.54 (0.18), residues: 1976 helix: 1.34 (0.18), residues: 890 sheet: 0.23 (0.33), residues: 226 loop : -0.61 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 188 HIS 0.006 0.001 HIS C 151 PHE 0.017 0.001 PHE A 4 TYR 0.013 0.001 TYR B 555 ARG 0.004 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7925 (mt-10) REVERT: A 294 ASP cc_start: 0.7752 (t0) cc_final: 0.7340 (t0) REVERT: A 382 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7647 (pt0) REVERT: A 399 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7646 (pt0) REVERT: B 108 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7929 (mp) REVERT: B 260 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7742 (ttp-110) REVERT: B 425 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8772 (t0) REVERT: B 656 GLU cc_start: 0.7220 (tt0) cc_final: 0.6987 (mm-30) REVERT: C 5 LYS cc_start: 0.7676 (mtpp) cc_final: 0.7469 (mtmm) REVERT: C 146 ASP cc_start: 0.6161 (p0) cc_final: 0.5546 (p0) REVERT: C 216 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7028 (mtm180) REVERT: C 368 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6285 (mtp-110) REVERT: C 493 ARG cc_start: 0.6152 (mtp180) cc_final: 0.5811 (mtt180) outliers start: 48 outliers final: 29 residues processed: 215 average time/residue: 1.4901 time to fit residues: 354.1060 Evaluate side-chains 210 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 532 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 191 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17053 Z= 0.166 Angle : 0.481 11.333 23147 Z= 0.246 Chirality : 0.039 0.158 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.264 73.550 2669 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.10 % Allowed : 25.70 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.59 (0.19), residues: 1976 helix: 1.39 (0.18), residues: 892 sheet: 0.22 (0.32), residues: 234 loop : -0.59 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.004 0.001 HIS C 151 PHE 0.010 0.001 PHE A 520 TYR 0.014 0.001 TYR B 555 ARG 0.006 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 183 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASP cc_start: 0.7755 (t0) cc_final: 0.7332 (t0) REVERT: A 382 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: A 399 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: B 108 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7888 (mp) REVERT: B 211 ARG cc_start: 0.7409 (mtp85) cc_final: 0.7140 (mtt-85) REVERT: B 260 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7743 (ttp-110) REVERT: B 287 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7642 (mtt90) REVERT: B 425 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8758 (t0) REVERT: B 656 GLU cc_start: 0.7206 (tt0) cc_final: 0.6991 (mm-30) REVERT: C 146 ASP cc_start: 0.6140 (p0) cc_final: 0.5573 (p0) REVERT: C 216 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7023 (mtm180) REVERT: C 368 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6289 (mtp-110) REVERT: C 493 ARG cc_start: 0.6167 (mtp180) cc_final: 0.5844 (mtt180) outliers start: 55 outliers final: 29 residues processed: 225 average time/residue: 1.4865 time to fit residues: 369.0175 Evaluate side-chains 212 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 532 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 121 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 chunk 174 optimal weight: 0.0570 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17053 Z= 0.142 Angle : 0.469 11.786 23147 Z= 0.240 Chirality : 0.038 0.148 2574 Planarity : 0.004 0.056 2870 Dihedral : 10.199 73.556 2668 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.59 % Allowed : 26.66 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 (0.19), residues: 1976 helix: 1.51 (0.18), residues: 884 sheet: 0.25 (0.33), residues: 236 loop : -0.52 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.003 0.001 HIS C 151 PHE 0.010 0.001 PHE A 520 TYR 0.013 0.001 TYR B 555 ARG 0.005 0.000 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASP cc_start: 0.7709 (t0) cc_final: 0.7200 (t0) REVERT: A 382 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: A 399 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: B 108 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7899 (mp) REVERT: B 260 ARG cc_start: 0.7978 (ttm110) cc_final: 0.7741 (ttp-110) REVERT: B 287 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7634 (mtt90) REVERT: B 425 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8707 (t0) REVERT: C 5 LYS cc_start: 0.7889 (mtmm) cc_final: 0.7489 (mtpp) REVERT: C 146 ASP cc_start: 0.6147 (p0) cc_final: 0.5584 (p0) REVERT: C 216 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7058 (mtm180) REVERT: C 368 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6307 (mtp-110) REVERT: C 415 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.4458 (mpp-170) REVERT: C 431 MET cc_start: 0.7298 (mtt) cc_final: 0.6929 (mtt) REVERT: C 493 ARG cc_start: 0.6183 (mtp180) cc_final: 0.5874 (mtt180) outliers start: 46 outliers final: 27 residues processed: 220 average time/residue: 1.4860 time to fit residues: 360.4299 Evaluate side-chains 207 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 532 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 161 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN B 184 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17053 Z= 0.196 Angle : 0.510 13.031 23147 Z= 0.257 Chirality : 0.039 0.196 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.206 73.537 2667 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.76 % Allowed : 26.66 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.60 (0.19), residues: 1976 helix: 1.39 (0.18), residues: 892 sheet: 0.25 (0.32), residues: 234 loop : -0.58 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.003 0.001 HIS C 151 PHE 0.011 0.001 PHE A 520 TYR 0.014 0.001 TYR B 555 ARG 0.006 0.000 ARG B 706 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 177 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2709 (ppp) cc_final: 0.1388 (ptm) REVERT: A 294 ASP cc_start: 0.7721 (t0) cc_final: 0.7210 (t0) REVERT: A 382 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7634 (pt0) REVERT: A 399 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: B 108 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7929 (mp) REVERT: B 260 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7754 (ttp-110) REVERT: B 287 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7645 (mtt90) REVERT: B 425 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8773 (t0) REVERT: C 5 LYS cc_start: 0.7872 (mtmm) cc_final: 0.7493 (mtpp) REVERT: C 146 ASP cc_start: 0.6183 (p0) cc_final: 0.5626 (p0) REVERT: C 216 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7020 (mtm180) REVERT: C 368 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6273 (mtp-110) REVERT: C 431 MET cc_start: 0.7303 (mtt) cc_final: 0.6938 (mtt) REVERT: C 467 MET cc_start: 0.6503 (mpm) cc_final: 0.5916 (mpt) REVERT: C 493 ARG cc_start: 0.6181 (mtp180) cc_final: 0.5848 (mtt180) outliers start: 49 outliers final: 30 residues processed: 216 average time/residue: 1.5036 time to fit residues: 359.8976 Evaluate side-chains 209 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 198 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 157 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 121 optimal weight: 0.0040 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN B 184 HIS C 447 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17053 Z= 0.188 Angle : 0.502 12.223 23147 Z= 0.255 Chirality : 0.039 0.186 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.206 73.579 2667 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.54 % Allowed : 26.94 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.60 (0.19), residues: 1976 helix: 1.37 (0.18), residues: 892 sheet: 0.29 (0.33), residues: 234 loop : -0.57 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 537 HIS 0.003 0.001 HIS C 151 PHE 0.011 0.001 PHE A 520 TYR 0.014 0.001 TYR B 555 ARG 0.005 0.000 ARG B 706 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 176 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2818 (ppp) cc_final: 0.1504 (ptm) REVERT: A 294 ASP cc_start: 0.7722 (t0) cc_final: 0.7208 (t0) REVERT: A 382 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: A 399 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: B 108 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7938 (mp) REVERT: B 111 MET cc_start: 0.8348 (ttp) cc_final: 0.8098 (ttp) REVERT: B 211 ARG cc_start: 0.7363 (mtt-85) cc_final: 0.7007 (mtp85) REVERT: B 248 ILE cc_start: 0.8611 (tt) cc_final: 0.8335 (pt) REVERT: B 260 ARG cc_start: 0.7985 (ttm110) cc_final: 0.7760 (ttp-110) REVERT: B 425 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8764 (t0) REVERT: C 5 LYS cc_start: 0.7894 (mtmm) cc_final: 0.7500 (mtpp) REVERT: C 146 ASP cc_start: 0.6171 (p0) cc_final: 0.5629 (p0) REVERT: C 216 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7012 (mtm180) REVERT: C 318 ARG cc_start: 0.7247 (mmt-90) cc_final: 0.6321 (mtm-85) REVERT: C 368 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6272 (mtp-110) REVERT: C 396 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6633 (tt0) REVERT: C 415 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.4424 (mpp-170) REVERT: C 431 MET cc_start: 0.7304 (mtt) cc_final: 0.6938 (mtt) REVERT: C 447 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6743 (tp-100) REVERT: C 467 MET cc_start: 0.6649 (mpm) cc_final: 0.6105 (mpt) REVERT: C 493 ARG cc_start: 0.6192 (mtp180) cc_final: 0.5827 (mtt180) outliers start: 45 outliers final: 27 residues processed: 210 average time/residue: 1.4936 time to fit residues: 345.9006 Evaluate side-chains 209 residues out of total 1775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 368 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 0.0020 chunk 145 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 20 optimal weight: 0.0470 chunk 29 optimal weight: 0.3980 chunk 138 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN B 184 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.150470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110128 restraints weight = 22626.524| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.67 r_work: 0.3068 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 17053 Z= 0.228 Angle : 0.703 58.683 23147 Z= 0.399 Chirality : 0.042 0.848 2574 Planarity : 0.004 0.057 2870 Dihedral : 10.207 73.545 2667 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.31 % Allowed : 27.45 % Favored : 70.24 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.15 % 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: 0.60 (0.19), residues: 1976 helix: 1.36 (0.18), residues: 894 sheet: 0.29 (0.33), residues: 234 loop : -0.56 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.003 0.001 HIS C 151 PHE 0.011 0.001 PHE A 520 TYR 0.014 0.001 TYR B 555 ARG 0.007 0.000 ARG B 706 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6328.96 seconds wall clock time: 114 minutes 20.29 seconds (6860.29 seconds total)