Starting phenix.real_space_refine on Tue Apr 9 00:52:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnq_17783/04_2024/8pnq_17783_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnq_17783/04_2024/8pnq_17783.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnq_17783/04_2024/8pnq_17783_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnq_17783/04_2024/8pnq_17783_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnq_17783/04_2024/8pnq_17783_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnq_17783/04_2024/8pnq_17783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnq_17783/04_2024/8pnq_17783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnq_17783/04_2024/8pnq_17783_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnq_17783/04_2024/8pnq_17783_updated.pdb" } resolution = 2.88 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 2 5.21 5 S 104 5.16 5 C 9214 2.51 5 N 2587 2.21 5 O 2956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B GLU 697": "OE1" <-> "OE2" Residue "B GLU 716": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14913 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: 5958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 744, 5950 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 713} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 744, 5950 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 713} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 6054 Chain: "C" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2024 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "V" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 758 Classifications: {'RNA': 36} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 9, 'rna3p_pyr': 14} Link IDs: {'rna2p': 13, 'rna3p': 22} Chain breaks: 1 Chain: "M" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 202 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 9} Link IDs: {'rna3p': 8} Chain: "G" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 192 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 7, 'TRANS': 17} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, '2KH': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALEU B 218 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 218 " occ=0.50 Time building chain proxies: 10.83, per 1000 atoms: 0.73 Number of scatterers: 14913 At special positions: 0 Unit cell: (96.6, 100.8, 141.96, 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 104 16.00 P 50 15.00 Mg 2 11.99 O 2956 8.00 N 2587 7.00 C 9214 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: 6.20 Conformation dependent library (CDL) restraints added in 3.4 seconds 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3268 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 16 sheets defined 45.4% alpha, 11.4% beta 11 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 7.00 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 11 through 24 removed outlier: 4.170A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 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 165 through 185 removed outlier: 3.685A pdb=" N ARG A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 removed outlier: 3.788A pdb=" N GLU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLY A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 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 350 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 414 Processing helix chain 'A' and resid 434 through 451 Processing helix chain 'A' and resid 454 through 475 Processing helix chain 'A' and resid 534 through 537 Processing helix chain 'A' and resid 572 through 603 removed outlier: 4.013A pdb=" N MET A 581 " --> pdb=" O TRP A 577 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ARG A 582 " --> pdb=" O GLY A 578 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N CYS A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 633 through 649 Processing helix chain 'A' and resid 653 through 673 removed outlier: 4.136A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 3.964A pdb=" N CYS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 715 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 15 through 21 removed outlier: 5.447A 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 116 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.671A 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 246 through 265 removed outlier: 4.561A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 292 Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 346 removed outlier: 4.685A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.597A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.260A pdb=" N ALA B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASN B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 375' 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: 4.033A 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 473 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 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 618 through 624 Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.782A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASP B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B 686 " --> pdb=" O ILE B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 703 No H-bonds generated for 'chain 'B' and resid 701 through 703' Processing helix chain 'B' and resid 714 through 732 Processing helix chain 'B' and resid 737 through 755 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 25 through 32 removed outlier: 4.194A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.093A 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 193 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 226 through 229 No H-bonds generated for 'chain 'C' and resid 226 through 229' Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing sheet with id= A, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.515A pdb=" N HIS A 144 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLY A 121 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N HIS A 146 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N THR A 123 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A 148 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.751A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.882A 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: 6.560A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.393A 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: 6.783A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.637A 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 181 Processing sheet with id= H, first strand: chain 'B' and resid 184 through 192 Processing sheet with id= I, first strand: chain 'B' and resid 224 through 228 Processing sheet with id= J, first strand: chain 'B' and resid 483 through 486 Processing sheet with id= K, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= L, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= M, first strand: chain 'B' and resid 489 through 492 Processing sheet with id= N, first strand: chain 'C' and resid 57 through 60 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 148 removed outlier: 6.695A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1693 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 6.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2393 1.31 - 1.44: 4242 1.44 - 1.57: 8393 1.57 - 1.69: 101 1.69 - 1.82: 180 Bond restraints: 15309 Sorted by residual: bond pdb=" C1' 2KH B 801 " pdb=" O4' 2KH B 801 " ideal model delta sigma weight residual 1.561 1.320 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C4' 2KH B 801 " pdb=" O4' 2KH B 801 " ideal model delta sigma weight residual 1.310 1.532 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C1' 2KH B 801 " pdb=" N1 2KH B 801 " ideal model delta sigma weight residual 1.322 1.437 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C3' 2KH B 801 " pdb=" C4' 2KH B 801 " ideal model delta sigma weight residual 1.643 1.538 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C4' 2KH B 801 " pdb=" C5' 2KH B 801 " ideal model delta sigma weight residual 1.526 1.430 0.096 2.00e-02 2.50e+03 2.33e+01 ... (remaining 15304 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.00: 709 107.00 - 113.76: 8517 113.76 - 120.51: 5974 120.51 - 127.26: 5430 127.26 - 134.02: 243 Bond angle restraints: 20873 Sorted by residual: angle pdb=" CB MET B 655 " pdb=" CG MET B 655 " pdb=" SD MET B 655 " ideal model delta sigma weight residual 112.70 122.24 -9.54 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N ILE A 30 " pdb=" CA ILE A 30 " pdb=" C ILE A 30 " ideal model delta sigma weight residual 113.42 110.23 3.19 1.17e+00 7.31e-01 7.43e+00 angle pdb=" CA ILE A 30 " pdb=" CB ILE A 30 " pdb=" CG1 ILE A 30 " ideal model delta sigma weight residual 110.40 114.29 -3.89 1.70e+00 3.46e-01 5.23e+00 angle pdb=" CG MET B 655 " pdb=" SD MET B 655 " pdb=" CE MET B 655 " ideal model delta sigma weight residual 100.90 105.78 -4.88 2.20e+00 2.07e-01 4.91e+00 angle pdb=" CA GLU A 181 " pdb=" CB GLU A 181 " pdb=" CG GLU A 181 " ideal model delta sigma weight residual 114.10 118.48 -4.38 2.00e+00 2.50e-01 4.80e+00 ... (remaining 20868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 7898 17.64 - 35.28: 988 35.28 - 52.92: 372 52.92 - 70.57: 124 70.57 - 88.21: 37 Dihedral angle restraints: 9419 sinusoidal: 4373 harmonic: 5046 Sorted by residual: dihedral pdb=" CA MET B 408 " pdb=" C MET B 408 " pdb=" N MET B 409 " pdb=" CA MET B 409 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CG ARG B 584 " pdb=" CD ARG B 584 " pdb=" NE ARG B 584 " pdb=" CZ ARG B 584 " ideal model delta sinusoidal sigma weight residual -90.00 -39.82 -50.18 2 1.50e+01 4.44e-03 1.26e+01 dihedral pdb=" CB GLU A 181 " pdb=" CG GLU A 181 " pdb=" CD GLU A 181 " pdb=" OE1 GLU A 181 " ideal model delta sinusoidal sigma weight residual 0.00 88.21 -88.21 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 9416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1569 0.031 - 0.061: 550 0.061 - 0.092: 115 0.092 - 0.122: 70 0.122 - 0.153: 11 Chirality restraints: 2315 Sorted by residual: chirality pdb=" C1' 2KH B 801 " pdb=" C2' 2KH B 801 " pdb=" N1 2KH B 801 " pdb=" O4' 2KH B 801 " both_signs ideal model delta sigma weight residual False 2.54 2.39 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA ILE C 67 " pdb=" N ILE C 67 " pdb=" C ILE C 67 " pdb=" CB ILE C 67 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA VAL B 368 " pdb=" N VAL B 368 " pdb=" C VAL B 368 " pdb=" CB VAL B 368 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2312 not shown) Planarity restraints: 2515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 584 " 0.221 9.50e-02 1.11e+02 9.92e-02 6.73e+00 pdb=" NE ARG B 584 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 584 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 584 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 584 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.024 2.00e-02 2.50e+03 1.04e-02 2.95e+00 pdb=" N9 A V 4 " 0.023 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.003 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 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.020 2.00e-02 2.50e+03 9.34e-03 2.40e+00 pdb=" N9 A V 7 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.002 2.00e-02 2.50e+03 ... (remaining 2512 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 65 2.46 - 3.07: 10084 3.07 - 3.68: 23093 3.68 - 4.29: 35611 4.29 - 4.90: 58466 Nonbonded interactions: 127319 Sorted by model distance: nonbonded pdb=" OD1 ASP B 305 " pdb="MG MG B 803 " model vdw 1.845 2.170 nonbonded pdb=" OD2 ASP B 305 " pdb="MG MG B 802 " model vdw 1.922 2.170 nonbonded pdb=" O1B 2KH B 801 " pdb="MG MG B 803 " model vdw 1.923 2.170 nonbonded pdb=" OG1 THR B 226 " pdb=" O ARG B 350 " model vdw 2.054 2.440 nonbonded pdb=" O1A 2KH B 801 " pdb="MG MG B 803 " model vdw 2.084 2.170 ... (remaining 127314 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=0.50 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: 2.410 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: 10.360 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 49.640 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 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 : 0.004 0.241 15309 Z= 0.254 Angle : 0.464 9.535 20873 Z= 0.240 Chirality : 0.036 0.153 2315 Planarity : 0.003 0.099 2515 Dihedral : 18.916 88.206 6151 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.01 % Allowed : 25.28 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.69 (0.21), residues: 1711 helix: 2.41 (0.19), residues: 811 sheet: 0.26 (0.36), residues: 193 loop : -0.13 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 49 HIS 0.003 0.001 HIS A 713 PHE 0.010 0.001 PHE A 53 TYR 0.014 0.001 TYR B 555 ARG 0.015 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6787 (mp0) cc_final: 0.6483 (pm20) REVERT: A 168 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7139 (mtm110) REVERT: A 201 ILE cc_start: 0.8780 (mm) cc_final: 0.8544 (mm) REVERT: A 348 ILE cc_start: 0.8747 (tp) cc_final: 0.8476 (tp) REVERT: C 243 MET cc_start: 0.8660 (mtp) cc_final: 0.8452 (mtp) outliers start: 30 outliers final: 25 residues processed: 218 average time/residue: 1.4285 time to fit residues: 340.6167 Evaluate side-chains 206 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 158 ASN B 184 HIS C 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15309 Z= 0.391 Angle : 0.561 8.551 20873 Z= 0.291 Chirality : 0.042 0.173 2315 Planarity : 0.004 0.043 2515 Dihedral : 12.659 84.710 2621 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.21 % Allowed : 22.94 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.26 (0.20), residues: 1711 helix: 1.94 (0.18), residues: 821 sheet: 0.20 (0.36), residues: 196 loop : -0.27 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 49 HIS 0.009 0.002 HIS B 32 PHE 0.014 0.002 PHE A 520 TYR 0.016 0.002 TYR B 557 ARG 0.009 0.001 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 191 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6619 (pm20) REVERT: A 168 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7097 (mtm110) REVERT: A 181 GLU cc_start: 0.7278 (tp30) cc_final: 0.7072 (tp30) REVERT: A 201 ILE cc_start: 0.8789 (mm) cc_final: 0.8580 (mm) REVERT: A 348 ILE cc_start: 0.8810 (tp) cc_final: 0.8555 (tp) REVERT: A 551 ARG cc_start: 0.7764 (mtm180) cc_final: 0.7549 (ttp80) REVERT: B 174 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8763 (mtp) REVERT: B 669 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7763 (ttmm) REVERT: C 53 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7386 (mpt) REVERT: G 11 SER cc_start: 0.4782 (OUTLIER) cc_final: 0.4499 (p) outliers start: 64 outliers final: 27 residues processed: 231 average time/residue: 1.2884 time to fit residues: 324.4779 Evaluate side-chains 213 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15309 Z= 0.202 Angle : 0.470 9.061 20873 Z= 0.245 Chirality : 0.038 0.168 2315 Planarity : 0.003 0.041 2515 Dihedral : 12.451 82.643 2605 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.69 % Allowed : 24.24 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.32 (0.20), residues: 1711 helix: 1.97 (0.18), residues: 820 sheet: 0.30 (0.37), residues: 196 loop : -0.23 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.004 0.001 HIS B 32 PHE 0.011 0.001 PHE A 520 TYR 0.015 0.001 TYR B 555 ARG 0.008 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 200 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6553 (pm20) REVERT: A 168 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7075 (mtm110) REVERT: A 181 GLU cc_start: 0.7368 (tp30) cc_final: 0.6855 (tp30) REVERT: A 191 PHE cc_start: 0.8051 (t80) cc_final: 0.7830 (t80) REVERT: A 201 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 293 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7858 (mm-30) REVERT: A 348 ILE cc_start: 0.8740 (tp) cc_final: 0.8498 (tp) REVERT: B 1 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7060 (tpp) REVERT: B 208 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7753 (pttp) REVERT: C 53 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7323 (mpt) REVERT: C 192 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: C 243 MET cc_start: 0.8629 (mtp) cc_final: 0.8415 (mtp) REVERT: G 20 THR cc_start: 0.9374 (m) cc_final: 0.9123 (p) outliers start: 56 outliers final: 25 residues processed: 236 average time/residue: 1.4415 time to fit residues: 371.4278 Evaluate side-chains 217 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 167 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN B 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15309 Z= 0.263 Angle : 0.489 9.593 20873 Z= 0.254 Chirality : 0.039 0.163 2315 Planarity : 0.004 0.042 2515 Dihedral : 12.415 82.368 2603 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.28 % Allowed : 24.30 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.24 (0.20), residues: 1711 helix: 1.90 (0.18), residues: 820 sheet: 0.26 (0.37), residues: 196 loop : -0.25 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.005 0.001 HIS B 32 PHE 0.012 0.001 PHE A 520 TYR 0.015 0.001 TYR B 555 ARG 0.008 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 190 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6578 (pm20) REVERT: A 168 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7083 (mtm110) REVERT: A 181 GLU cc_start: 0.7498 (tp30) cc_final: 0.6809 (tp30) REVERT: A 201 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8579 (mm) REVERT: A 348 ILE cc_start: 0.8747 (tp) cc_final: 0.8507 (tp) REVERT: B 1 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7128 (tpp) REVERT: B 208 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7768 (pttp) REVERT: B 669 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7777 (ttmm) REVERT: C 53 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7348 (mpt) REVERT: C 146 ASP cc_start: 0.8511 (p0) cc_final: 0.8175 (p0) REVERT: C 192 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: C 243 MET cc_start: 0.8646 (mtp) cc_final: 0.8426 (mtp) REVERT: G 20 THR cc_start: 0.9410 (m) cc_final: 0.9151 (p) outliers start: 65 outliers final: 29 residues processed: 234 average time/residue: 1.4703 time to fit residues: 376.0352 Evaluate side-chains 224 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain G residue 4 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 115 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15309 Z= 0.182 Angle : 0.458 10.322 20873 Z= 0.238 Chirality : 0.038 0.153 2315 Planarity : 0.003 0.041 2515 Dihedral : 12.300 81.432 2602 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.37 % Allowed : 25.21 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.33 (0.20), residues: 1711 helix: 1.92 (0.18), residues: 822 sheet: 0.29 (0.37), residues: 196 loop : -0.16 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 49 HIS 0.003 0.001 HIS A 713 PHE 0.010 0.001 PHE A 520 TYR 0.015 0.001 TYR B 555 ARG 0.010 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 200 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6541 (pm20) REVERT: A 181 GLU cc_start: 0.7523 (tp30) cc_final: 0.6894 (tp30) REVERT: A 201 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8586 (mm) REVERT: A 348 ILE cc_start: 0.8721 (tp) cc_final: 0.8474 (tp) REVERT: B 1 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7109 (tpp) REVERT: B 208 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7756 (pttp) REVERT: C 53 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7256 (mpt) REVERT: C 146 ASP cc_start: 0.8529 (p0) cc_final: 0.8179 (p0) REVERT: C 192 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: C 243 MET cc_start: 0.8630 (mtp) cc_final: 0.8407 (mtp) REVERT: G 11 SER cc_start: 0.4809 (OUTLIER) cc_final: 0.4538 (p) REVERT: G 20 THR cc_start: 0.9387 (m) cc_final: 0.9158 (p) outliers start: 51 outliers final: 24 residues processed: 234 average time/residue: 1.4375 time to fit residues: 367.6700 Evaluate side-chains 219 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.0270 chunk 167 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15309 Z= 0.169 Angle : 0.446 7.074 20873 Z= 0.233 Chirality : 0.037 0.152 2315 Planarity : 0.003 0.042 2515 Dihedral : 12.237 79.967 2601 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.69 % Allowed : 25.15 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.36 (0.20), residues: 1711 helix: 1.94 (0.18), residues: 823 sheet: 0.26 (0.37), residues: 202 loop : -0.10 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 49 HIS 0.003 0.001 HIS A 713 PHE 0.013 0.001 PHE A 53 TYR 0.019 0.001 TYR B 557 ARG 0.010 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 194 time to evaluate : 1.614 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6543 (pm20) REVERT: A 168 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7070 (mtm110) REVERT: A 181 GLU cc_start: 0.7536 (tp30) cc_final: 0.6954 (tp30) REVERT: A 191 PHE cc_start: 0.8016 (t80) cc_final: 0.7758 (t80) REVERT: A 201 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8607 (mm) REVERT: B 1 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7186 (tpp) REVERT: B 208 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7758 (pttp) REVERT: C 53 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7254 (mpt) REVERT: C 146 ASP cc_start: 0.8539 (p0) cc_final: 0.8155 (p0) REVERT: C 192 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: C 243 MET cc_start: 0.8623 (mtp) cc_final: 0.8399 (mtp) REVERT: G 11 SER cc_start: 0.4829 (OUTLIER) cc_final: 0.4555 (p) REVERT: G 20 THR cc_start: 0.9390 (m) cc_final: 0.9173 (p) outliers start: 56 outliers final: 29 residues processed: 232 average time/residue: 1.4067 time to fit residues: 357.2388 Evaluate side-chains 221 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 0.0050 chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15309 Z= 0.137 Angle : 0.443 12.486 20873 Z= 0.230 Chirality : 0.037 0.146 2315 Planarity : 0.003 0.043 2515 Dihedral : 12.169 79.469 2601 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.92 % Allowed : 25.92 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.45 (0.20), residues: 1711 helix: 2.01 (0.18), residues: 822 sheet: 0.32 (0.37), residues: 203 loop : -0.06 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.003 0.000 HIS A 713 PHE 0.009 0.001 PHE A 520 TYR 0.018 0.001 TYR B 557 ARG 0.010 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 206 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6527 (pm20) REVERT: A 181 GLU cc_start: 0.7565 (tp30) cc_final: 0.6943 (tp30) REVERT: B 208 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7742 (pttp) REVERT: B 655 MET cc_start: 0.6854 (mmm) cc_final: 0.6582 (mmp) REVERT: C 53 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7222 (mpt) REVERT: C 146 ASP cc_start: 0.8532 (p0) cc_final: 0.8138 (p0) REVERT: C 192 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: C 243 MET cc_start: 0.8612 (mtp) cc_final: 0.8383 (mtp) REVERT: G 11 SER cc_start: 0.4909 (OUTLIER) cc_final: 0.4642 (p) outliers start: 44 outliers final: 24 residues processed: 238 average time/residue: 1.4025 time to fit residues: 365.8870 Evaluate side-chains 223 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 GLN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15309 Z= 0.278 Angle : 0.502 11.101 20873 Z= 0.259 Chirality : 0.039 0.165 2315 Planarity : 0.004 0.043 2515 Dihedral : 12.241 81.164 2600 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.69 % Allowed : 25.53 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.30 (0.20), residues: 1711 helix: 1.88 (0.18), residues: 822 sheet: 0.25 (0.37), residues: 203 loop : -0.13 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.005 0.001 HIS B 32 PHE 0.011 0.001 PHE A 520 TYR 0.025 0.002 TYR B 557 ARG 0.009 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 190 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6543 (pm20) REVERT: A 125 ARG cc_start: 0.7359 (ptp-170) cc_final: 0.7032 (ptp-170) REVERT: A 134 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8322 (tptm) REVERT: A 168 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7031 (mtm110) REVERT: A 181 GLU cc_start: 0.7661 (tp30) cc_final: 0.7086 (tp30) REVERT: B 208 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7745 (pttp) REVERT: C 53 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7249 (mpt) REVERT: C 137 ASN cc_start: 0.8317 (t0) cc_final: 0.8088 (t0) REVERT: C 146 ASP cc_start: 0.8638 (p0) cc_final: 0.8203 (p0) REVERT: C 243 MET cc_start: 0.8640 (mtp) cc_final: 0.8410 (mtp) REVERT: G 11 SER cc_start: 0.5007 (OUTLIER) cc_final: 0.4722 (p) outliers start: 56 outliers final: 30 residues processed: 231 average time/residue: 1.4728 time to fit residues: 371.4159 Evaluate side-chains 221 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 9.9990 chunk 145 optimal weight: 0.7980 chunk 155 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 GLN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15309 Z= 0.152 Angle : 0.452 7.752 20873 Z= 0.236 Chirality : 0.037 0.150 2315 Planarity : 0.003 0.042 2515 Dihedral : 12.187 80.112 2600 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.72 % Allowed : 26.38 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.38 (0.20), residues: 1711 helix: 1.92 (0.18), residues: 823 sheet: 0.38 (0.37), residues: 202 loop : -0.10 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.003 0.001 HIS A 713 PHE 0.009 0.001 PHE A 520 TYR 0.023 0.001 TYR B 557 ARG 0.010 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 196 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6483 (pm20) REVERT: A 125 ARG cc_start: 0.7359 (ptp-170) cc_final: 0.7014 (ptp-170) REVERT: A 134 LYS cc_start: 0.8528 (mmmt) cc_final: 0.8314 (tptm) REVERT: A 181 GLU cc_start: 0.7664 (tp30) cc_final: 0.7032 (tp30) REVERT: B 208 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7754 (pttp) REVERT: C 53 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7144 (mpt) REVERT: C 137 ASN cc_start: 0.8311 (t0) cc_final: 0.8085 (t0) REVERT: C 146 ASP cc_start: 0.8576 (p0) cc_final: 0.8140 (p0) REVERT: C 243 MET cc_start: 0.8620 (mtp) cc_final: 0.8394 (mtp) REVERT: G 11 SER cc_start: 0.4999 (OUTLIER) cc_final: 0.4718 (p) outliers start: 41 outliers final: 28 residues processed: 232 average time/residue: 1.4674 time to fit residues: 371.2315 Evaluate side-chains 223 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 0.0770 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 109 optimal weight: 0.0970 overall best weight: 1.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 GLN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15309 Z= 0.232 Angle : 0.492 12.193 20873 Z= 0.253 Chirality : 0.038 0.156 2315 Planarity : 0.004 0.046 2515 Dihedral : 12.213 80.999 2600 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.79 % Allowed : 26.18 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.31 (0.20), residues: 1711 helix: 1.86 (0.18), residues: 823 sheet: 0.34 (0.37), residues: 202 loop : -0.13 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.004 0.001 HIS B 32 PHE 0.014 0.001 PHE A 105 TYR 0.026 0.001 TYR B 557 ARG 0.010 0.000 ARG B 584 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 1.666 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6513 (pm20) REVERT: A 134 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8295 (tptm) REVERT: A 168 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7058 (mtm110) REVERT: A 181 GLU cc_start: 0.7639 (tp30) cc_final: 0.7038 (tp30) REVERT: B 1 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7122 (tpp) REVERT: B 208 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7728 (pttp) REVERT: B 655 MET cc_start: 0.6964 (mmm) cc_final: 0.6636 (mmp) REVERT: C 53 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7180 (mpt) REVERT: C 137 ASN cc_start: 0.8335 (t0) cc_final: 0.8101 (t0) REVERT: C 146 ASP cc_start: 0.8558 (p0) cc_final: 0.8072 (p0) REVERT: C 243 MET cc_start: 0.8655 (mtp) cc_final: 0.8425 (mtp) REVERT: G 11 SER cc_start: 0.5099 (OUTLIER) cc_final: 0.4779 (p) outliers start: 42 outliers final: 28 residues processed: 226 average time/residue: 1.4939 time to fit residues: 369.2407 Evaluate side-chains 220 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.0020 chunk 120 optimal weight: 2.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN B 582 GLN C 42 ASN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.077582 restraints weight = 39704.556| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.70 r_work: 0.2734 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15309 Z= 0.180 Angle : 0.472 12.055 20873 Z= 0.244 Chirality : 0.037 0.153 2315 Planarity : 0.003 0.044 2515 Dihedral : 12.199 80.623 2600 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.79 % Allowed : 26.12 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.33 (0.20), residues: 1711 helix: 1.87 (0.18), residues: 823 sheet: 0.39 (0.37), residues: 202 loop : -0.11 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.003 0.001 HIS B 32 PHE 0.019 0.001 PHE A 105 TYR 0.025 0.001 TYR B 557 ARG 0.010 0.000 ARG B 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5836.29 seconds wall clock time: 105 minutes 22.46 seconds (6322.46 seconds total)