Starting phenix.real_space_refine on Sat Feb 17 12:21:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2024/6t0v_10360_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2024/6t0v_10360.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2024/6t0v_10360_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2024/6t0v_10360_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2024/6t0v_10360_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2024/6t0v_10360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2024/6t0v_10360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2024/6t0v_10360_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2024/6t0v_10360_updated.pdb" } resolution = 3.02 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= 0.006 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 48 5.49 5 Mg 5 5.21 5 S 108 5.16 5 C 11562 2.51 5 N 3253 2.21 5 O 3628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 707": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 427": "NH1" <-> "NH2" Residue "C GLU 662": "OE1" <-> "OE2" Residue "C GLU 682": "OE1" <-> "OE2" Residue "C ARG 737": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18604 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5746 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 25, 'TRANS': 679} Chain breaks: 2 Chain: "B" Number of atoms: 5950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5950 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 716} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 5878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5878 Classifications: {'peptide': 740} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 709} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "V" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 307 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain: "R" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 3, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 10} Chain: "M" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 296 Unusual residues: {'GTG': 1} Classifications: {'RNA': 11, 'undetermined': 1} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 1} Link IDs: {'rna3p': 10, None: 1} Not linked: pdbres="GTG M 1 " pdbres=" A M 2 " Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' MG': 2, 'M4H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 3, '2KH': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 10.51, per 1000 atoms: 0.56 Number of scatterers: 18604 At special positions: 0 Unit cell: (120.28, 127.594, 116.216, 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 108 16.00 P 48 15.00 Mg 5 11.99 O 3628 8.00 N 3253 7.00 C 11562 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.43 Conformation dependent library (CDL) restraints added in 3.3 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 20 sheets defined 40.0% alpha, 12.1% beta 11 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 8.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 5 No H-bonds generated for 'chain 'A' and resid 2 through 5' Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.908A pdb=" N TYR A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 49 removed outlier: 3.556A pdb=" N ALA A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 209 through 218 removed outlier: 3.575A pdb=" N SER A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) 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 313 removed outlier: 3.964A pdb=" N THR A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 449 through 470 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 529 through 532 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 576 through 598 removed outlier: 3.633A pdb=" N SER A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 584 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN A 585 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 587 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 593 " --> pdb=" O MET A 590 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 596 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 598 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 628 through 644 Processing helix chain 'A' and resid 648 through 668 removed outlier: 4.096A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 693 through 712 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 18 through 21 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 removed outlier: 3.596A pdb=" N GLN B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.961A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU B 175 " --> pdb=" O LEU 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: 4.263A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 292 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: 4.709A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 383 through 395 removed outlier: 5.500A pdb=" N HIS B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.740A pdb=" N VAL B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY B 427 " --> pdb=" O VAL 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 removed outlier: 3.654A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 519 through 535 removed outlier: 3.847A pdb=" N MET B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 573 through 581 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 618 through 624 Processing helix chain 'B' and resid 684 through 697 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 753 Processing helix chain 'C' and resid 2 through 12 removed outlier: 3.684A pdb=" N LYS C 12 " --> pdb=" O MET C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 27 through 29 No H-bonds generated for 'chain 'C' and resid 27 through 29' Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.546A pdb=" N MET C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.632A pdb=" N MET C 66 " --> pdb=" O ILE C 63 " (cutoff:3.500A) 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 126 Processing helix chain 'C' and resid 156 through 166 Processing helix chain 'C' and resid 180 through 192 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 252 through 272 removed outlier: 4.149A pdb=" N GLN C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 286 removed outlier: 3.729A pdb=" N HIS C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 297 No H-bonds generated for 'chain 'C' and resid 294 through 297' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 391 through 404 removed outlier: 3.559A pdb=" N LEU C 395 " --> pdb=" O LEU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 440 removed outlier: 3.909A pdb=" N LYS C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) 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 helix chain 'C' and resid 542 through 555 Processing helix chain 'C' and resid 557 through 565 removed outlier: 3.697A pdb=" N THR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 577 No H-bonds generated for 'chain 'C' and resid 575 through 577' Processing helix chain 'C' and resid 588 through 605 Processing helix chain 'C' and resid 612 through 621 removed outlier: 3.860A pdb=" N LEU C 618 " --> pdb=" O GLN C 614 " (cutoff:3.500A) Proline residue: C 620 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 109 through 111 Processing sheet with id= B, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.377A pdb=" N ILE A 480 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N PHE A 498 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 478 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 497 through 501 removed outlier: 6.421A pdb=" N LEU A 558 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU A 539 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A 560 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL A 537 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU A 539 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE A 322 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 614 through 618 removed outlier: 6.689A pdb=" N GLU A 624 " --> pdb=" O ILE A 616 " (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 180 through 192 removed outlier: 3.513A pdb=" N VAL B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.691A pdb=" N VAL B 348 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR B 226 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ARG B 350 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N THR B 228 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 483 through 486 removed outlier: 3.500A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= K, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= L, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= M, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= N, first strand: chain 'C' and resid 287 through 289 Processing sheet with id= O, first strand: chain 'C' and resid 323 through 325 removed outlier: 3.718A pdb=" N PHE C 323 " --> pdb=" O PHE C 330 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU C 362 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 373 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN C 383 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLY C 377 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 338 through 345 Processing sheet with id= Q, first strand: chain 'C' and resid 635 through 640 Processing sheet with id= R, first strand: chain 'C' and resid 656 through 659 removed outlier: 3.818A pdb=" N GLY C 673 " --> pdb=" O ILE C 665 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL C 667 " --> pdb=" O SER C 671 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N SER C 671 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 694 through 696 removed outlier: 4.263A pdb=" N GLY C 727 " --> pdb=" O ASP C 730 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL C 732 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU C 725 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL C 734 " --> pdb=" O ASN C 723 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASN C 723 " --> pdb=" O VAL C 734 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.349A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 7.88 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: 3005 1.31 - 1.43: 5221 1.43 - 1.56: 10544 1.56 - 1.69: 92 1.69 - 1.81: 191 Bond restraints: 19053 Sorted by residual: bond pdb=" C3D GTG M 1 " pdb=" C4D GTG M 1 " ideal model delta sigma weight residual 1.298 1.550 -0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C2E GTG M 1 " pdb=" C3E GTG M 1 " ideal model delta sigma weight residual 1.254 1.494 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C1' 2KH B 801 " pdb=" O4' 2KH B 801 " ideal model delta sigma weight residual 1.561 1.321 0.240 2.00e-02 2.50e+03 1.44e+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=" C5B GTG M 1 " pdb=" C6B GTG M 1 " ideal model delta sigma weight residual 1.538 1.325 0.213 2.00e-02 2.50e+03 1.14e+02 ... (remaining 19048 not shown) Histogram of bond angle deviations from ideal: 95.93 - 104.67: 500 104.67 - 113.41: 10695 113.41 - 122.16: 11168 122.16 - 130.90: 3468 130.90 - 139.64: 93 Bond angle restraints: 25924 Sorted by residual: angle pdb=" C1D GTG M 1 " pdb=" N9A GTG M 1 " pdb=" C4A GTG M 1 " ideal model delta sigma weight residual 93.21 126.25 -33.04 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C1D GTG M 1 " pdb=" N9A GTG M 1 " pdb=" C8A GTG M 1 " ideal model delta sigma weight residual 157.61 125.32 32.29 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C1E GTG M 1 " pdb=" N9B GTG M 1 " pdb=" C4B GTG M 1 " ideal model delta sigma weight residual 152.69 128.62 24.07 3.00e+00 1.11e-01 6.44e+01 angle pdb=" C1E GTG M 1 " pdb=" N9B GTG M 1 " pdb=" C8B GTG M 1 " ideal model delta sigma weight residual 99.21 123.21 -24.00 3.00e+00 1.11e-01 6.40e+01 angle pdb=" N18 M4H A 801 " pdb=" C19 M4H A 801 " pdb=" N26 M4H A 801 " ideal model delta sigma weight residual 125.81 139.64 -13.83 3.00e+00 1.11e-01 2.13e+01 ... (remaining 25919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.19: 10764 24.19 - 48.39: 655 48.39 - 72.58: 191 72.58 - 96.78: 27 96.78 - 120.97: 1 Dihedral angle restraints: 11638 sinusoidal: 5270 harmonic: 6368 Sorted by residual: dihedral pdb=" CA MET B 409 " pdb=" C MET B 409 " pdb=" N GLY B 410 " pdb=" CA GLY B 410 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA PHE B 447 " pdb=" C PHE B 447 " pdb=" N ALA B 448 " pdb=" CA ALA B 448 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA SER C 366 " pdb=" C SER C 366 " pdb=" N GLY C 367 " pdb=" CA GLY C 367 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 11635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2597 0.081 - 0.162: 274 0.162 - 0.242: 11 0.242 - 0.323: 2 0.323 - 0.404: 1 Chirality restraints: 2885 Sorted by residual: chirality pdb=" C3D GTG M 1 " pdb=" C2D GTG M 1 " pdb=" C4D GTG M 1 " pdb=" O3D GTG M 1 " both_signs ideal model delta sigma weight residual False -2.38 -2.78 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C3E GTG M 1 " pdb=" C2E GTG M 1 " pdb=" C4E GTG M 1 " pdb=" O3E GTG M 1 " both_signs ideal model delta sigma weight residual False -2.43 -2.74 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C2E GTG M 1 " pdb=" C1E GTG M 1 " pdb=" C3E GTG M 1 " pdb=" O2E GTG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2882 not shown) Planarity restraints: 3163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 329 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO B 330 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.035 2.00e-02 2.50e+03 1.61e-02 7.15e+00 pdb=" N9 A V 7 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 7 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.02e+00 pdb=" N PRO A 620 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.037 5.00e-02 4.00e+02 ... (remaining 3160 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 136 2.47 - 3.08: 11163 3.08 - 3.68: 28823 3.68 - 4.29: 45599 4.29 - 4.90: 73505 Nonbonded interactions: 159226 Sorted by model distance: nonbonded pdb=" O11 M4H A 801 " pdb="MG MG A 802 " model vdw 1.859 2.170 nonbonded pdb=" OD1 ASP A 108 " pdb="MG MG A 803 " model vdw 1.871 2.170 nonbonded pdb=" OE2 GLU A 119 " pdb="MG MG A 802 " model vdw 1.873 2.170 nonbonded pdb=" OD2 ASP A 108 " pdb="MG MG A 802 " model vdw 1.884 2.170 nonbonded pdb=" O ILE A 120 " pdb="MG MG A 802 " model vdw 1.885 2.170 ... (remaining 159221 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: 1.910 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: 7.950 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 55.430 Find NCS groups from input model: 0.740 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 : 0.009 0.252 19053 Z= 0.539 Angle : 0.874 33.039 25924 Z= 0.454 Chirality : 0.050 0.404 2885 Planarity : 0.006 0.068 3163 Dihedral : 16.758 120.971 7522 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 7.38 % Allowed : 10.22 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -3.31 (0.14), residues: 2178 helix: -2.14 (0.12), residues: 949 sheet: -1.76 (0.28), residues: 247 loop : -2.26 (0.17), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 49 HIS 0.006 0.001 HIS C 27 PHE 0.025 0.002 PHE C 656 TYR 0.021 0.002 TYR B 497 ARG 0.006 0.001 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 398 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6529 (tt0) REVERT: A 189 ASP cc_start: 0.6533 (m-30) cc_final: 0.6019 (p0) REVERT: A 315 TRP cc_start: 0.7336 (OUTLIER) cc_final: 0.6736 (p90) REVERT: A 381 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6748 (mm-30) REVERT: A 384 ASP cc_start: 0.7048 (p0) cc_final: 0.6201 (t0) REVERT: A 418 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8215 (mm) REVERT: A 474 GLU cc_start: 0.7387 (mp0) cc_final: 0.7144 (mp0) REVERT: A 506 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7815 (mt) REVERT: A 540 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7908 (pt) REVERT: A 553 MET cc_start: 0.7629 (ttm) cc_final: 0.7283 (ttm) REVERT: A 604 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6496 (tt0) REVERT: A 616 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8410 (pp) REVERT: B 108 GLN cc_start: 0.7164 (tp-100) cc_final: 0.6735 (pt0) REVERT: B 152 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7318 (mtmt) REVERT: B 310 ASN cc_start: 0.7400 (p0) cc_final: 0.7151 (p0) REVERT: B 670 ARG cc_start: 0.5867 (ptm160) cc_final: 0.5573 (mtp180) REVERT: B 694 GLN cc_start: 0.8087 (mt0) cc_final: 0.7839 (mt0) REVERT: B 721 ARG cc_start: 0.8431 (tpt-90) cc_final: 0.8138 (tpt170) REVERT: C 51 MET cc_start: 0.8017 (mmm) cc_final: 0.7691 (mmp) REVERT: C 217 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8933 (m-80) REVERT: C 328 TYR cc_start: 0.7420 (m-80) cc_final: 0.7162 (m-80) REVERT: C 339 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6098 (ptm-80) REVERT: C 364 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.7042 (m110) REVERT: C 458 MET cc_start: 0.3844 (mmm) cc_final: 0.3168 (mtp) REVERT: C 630 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6431 (mtp85) outliers start: 143 outliers final: 66 residues processed: 505 average time/residue: 0.3569 time to fit residues: 259.1905 Evaluate side-chains 373 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 295 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 725 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 0.0770 chunk 173 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 128 optimal weight: 0.0970 chunk 200 optimal weight: 7.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 228 GLN A 256 GLN A 403 GLN B 58 ASN B 127 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN B 452 ASN C 13 ASN C 39 GLN C 75 ASN C 160 GLN C 182 GLN ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN C 524 GLN C 581 GLN C 632 GLN C 657 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19053 Z= 0.126 Angle : 0.471 13.950 25924 Z= 0.243 Chirality : 0.038 0.155 2885 Planarity : 0.004 0.049 3163 Dihedral : 13.344 116.393 3242 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.92 % Allowed : 14.09 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.63 (0.16), residues: 2178 helix: -0.31 (0.16), residues: 949 sheet: -1.25 (0.29), residues: 248 loop : -1.76 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 188 HIS 0.004 0.001 HIS A 505 PHE 0.012 0.001 PHE C 330 TYR 0.015 0.001 TYR A 131 ARG 0.011 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 327 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7559 (tp) REVERT: A 315 TRP cc_start: 0.7328 (OUTLIER) cc_final: 0.6796 (p90) REVERT: A 384 ASP cc_start: 0.6579 (p0) cc_final: 0.5933 (t0) REVERT: A 474 GLU cc_start: 0.7381 (mp0) cc_final: 0.7132 (mp0) REVERT: A 571 LYS cc_start: 0.7773 (tttp) cc_final: 0.7542 (tptt) REVERT: A 616 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8625 (tp) REVERT: B 6 MET cc_start: 0.7865 (mtt) cc_final: 0.7661 (mtt) REVERT: B 108 GLN cc_start: 0.7049 (tp-100) cc_final: 0.6610 (pt0) REVERT: B 286 ILE cc_start: 0.8593 (mm) cc_final: 0.8377 (mm) REVERT: B 310 ASN cc_start: 0.7238 (p0) cc_final: 0.6981 (p0) REVERT: B 409 MET cc_start: 0.8121 (tpt) cc_final: 0.7845 (tpt) REVERT: B 670 ARG cc_start: 0.5973 (ptm160) cc_final: 0.5626 (mtp180) REVERT: B 694 GLN cc_start: 0.7946 (mt0) cc_final: 0.7669 (mt0) REVERT: C 157 ARG cc_start: 0.6712 (mtm180) cc_final: 0.6387 (mtt180) REVERT: C 188 GLU cc_start: 0.6578 (tp30) cc_final: 0.6306 (tp30) REVERT: C 217 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8824 (m-80) REVERT: C 292 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6312 (tm-30) REVERT: C 364 ASN cc_start: 0.7059 (OUTLIER) cc_final: 0.6824 (m110) REVERT: C 410 MET cc_start: 0.2394 (tmm) cc_final: 0.2186 (tmm) REVERT: C 458 MET cc_start: 0.3678 (mmm) cc_final: 0.3155 (mtp) outliers start: 76 outliers final: 44 residues processed: 380 average time/residue: 0.3639 time to fit residues: 199.5983 Evaluate side-chains 338 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 288 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 680 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 201 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 161 optimal weight: 0.0770 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 228 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 HIS C 524 GLN C 663 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19053 Z= 0.231 Angle : 0.517 12.951 25924 Z= 0.265 Chirality : 0.041 0.150 2885 Planarity : 0.004 0.049 3163 Dihedral : 12.783 109.782 3159 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.90 % Allowed : 14.55 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.04 (0.17), residues: 2178 helix: 0.28 (0.17), residues: 951 sheet: -0.94 (0.31), residues: 244 loop : -1.58 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 188 HIS 0.004 0.001 HIS A 360 PHE 0.014 0.001 PHE C 330 TYR 0.014 0.001 TYR B 497 ARG 0.009 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 284 time to evaluate : 2.501 Fit side-chains revert: symmetry clash REVERT: A 61 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7605 (tp) REVERT: A 83 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: A 315 TRP cc_start: 0.7399 (OUTLIER) cc_final: 0.6874 (p90) REVERT: A 384 ASP cc_start: 0.6988 (p0) cc_final: 0.6125 (t0) REVERT: A 474 GLU cc_start: 0.7588 (mp0) cc_final: 0.7301 (mp0) REVERT: A 616 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8462 (pp) REVERT: B 108 GLN cc_start: 0.7135 (tp-100) cc_final: 0.6550 (pt0) REVERT: B 112 ASP cc_start: 0.7043 (m-30) cc_final: 0.6592 (m-30) REVERT: B 310 ASN cc_start: 0.7245 (p0) cc_final: 0.6990 (p0) REVERT: B 670 ARG cc_start: 0.5951 (ptm160) cc_final: 0.5576 (mtp180) REVERT: B 694 GLN cc_start: 0.7992 (mt0) cc_final: 0.7709 (mt0) REVERT: C 146 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7093 (t0) REVERT: C 183 LEU cc_start: 0.8479 (mt) cc_final: 0.8239 (mp) REVERT: C 217 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8846 (m-80) REVERT: C 292 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6945 (mm-30) REVERT: C 364 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.6898 (m110) REVERT: C 458 MET cc_start: 0.3690 (mmm) cc_final: 0.3177 (mtp) REVERT: C 476 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5636 (ttp) outliers start: 95 outliers final: 63 residues processed: 351 average time/residue: 0.3640 time to fit residues: 186.4829 Evaluate side-chains 345 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 273 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 213 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 527 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN C 406 GLN C 429 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19053 Z= 0.316 Angle : 0.561 13.047 25924 Z= 0.288 Chirality : 0.042 0.158 2885 Planarity : 0.004 0.043 3163 Dihedral : 12.900 104.952 3155 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.57 % Allowed : 15.53 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.89 (0.17), residues: 2178 helix: 0.39 (0.17), residues: 952 sheet: -0.82 (0.31), residues: 253 loop : -1.49 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 188 HIS 0.005 0.001 HIS A 360 PHE 0.015 0.002 PHE C 656 TYR 0.015 0.002 TYR B 497 ARG 0.003 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 280 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: A 61 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7587 (tp) REVERT: A 83 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: A 160 GLU cc_start: 0.6583 (mp0) cc_final: 0.6321 (mp0) REVERT: A 249 MET cc_start: 0.8601 (ttp) cc_final: 0.8359 (ttm) REVERT: A 315 TRP cc_start: 0.7412 (OUTLIER) cc_final: 0.6862 (p90) REVERT: A 384 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6102 (t0) REVERT: A 474 GLU cc_start: 0.7684 (mp0) cc_final: 0.7406 (mp0) REVERT: A 506 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7720 (mt) REVERT: A 616 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8596 (pp) REVERT: B 1 MET cc_start: 0.7217 (tmm) cc_final: 0.6610 (tmm) REVERT: B 108 GLN cc_start: 0.7121 (tp-100) cc_final: 0.6664 (pt0) REVERT: B 310 ASN cc_start: 0.7306 (p0) cc_final: 0.7060 (p0) REVERT: B 367 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: B 670 ARG cc_start: 0.6030 (ptm160) cc_final: 0.5616 (mtp180) REVERT: B 694 GLN cc_start: 0.8052 (mt0) cc_final: 0.7780 (mt0) REVERT: C 51 MET cc_start: 0.8152 (mmm) cc_final: 0.7835 (mmp) REVERT: C 146 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7117 (t0) REVERT: C 183 LEU cc_start: 0.8538 (mt) cc_final: 0.8327 (mp) REVERT: C 217 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8847 (m-80) REVERT: C 364 ASN cc_start: 0.7393 (OUTLIER) cc_final: 0.7023 (m110) REVERT: C 406 GLN cc_start: 0.6345 (mt0) cc_final: 0.6084 (mt0) REVERT: C 458 MET cc_start: 0.3807 (mmm) cc_final: 0.3220 (mtp) REVERT: C 476 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.5752 (ttp) REVERT: C 522 GLN cc_start: 0.7461 (tp40) cc_final: 0.7237 (tp-100) REVERT: C 630 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6384 (mmm160) REVERT: C 663 ASN cc_start: 0.8256 (t0) cc_final: 0.8029 (t0) outliers start: 108 outliers final: 77 residues processed: 357 average time/residue: 0.3683 time to fit residues: 193.5313 Evaluate side-chains 357 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 268 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 182 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 19053 Z= 0.365 Angle : 0.591 13.259 25924 Z= 0.304 Chirality : 0.043 0.167 2885 Planarity : 0.005 0.043 3163 Dihedral : 13.017 102.124 3155 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.93 % Allowed : 15.94 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.91 (0.18), residues: 2178 helix: 0.34 (0.17), residues: 955 sheet: -0.79 (0.31), residues: 249 loop : -1.48 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 188 HIS 0.006 0.001 HIS A 360 PHE 0.017 0.002 PHE C 656 TYR 0.015 0.002 TYR A 496 ARG 0.005 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 279 time to evaluate : 2.165 Fit side-chains REVERT: A 55 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6180 (p0) REVERT: A 83 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: A 160 GLU cc_start: 0.6655 (mp0) cc_final: 0.6066 (mp0) REVERT: A 189 ASP cc_start: 0.6473 (m-30) cc_final: 0.5946 (p0) REVERT: A 249 MET cc_start: 0.8625 (ttp) cc_final: 0.8365 (ttm) REVERT: A 315 TRP cc_start: 0.7403 (OUTLIER) cc_final: 0.6906 (p90) REVERT: A 384 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6180 (t0) REVERT: A 474 GLU cc_start: 0.7762 (mp0) cc_final: 0.7483 (mp0) REVERT: A 506 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7774 (mt) REVERT: A 540 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7868 (pp) REVERT: A 616 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8644 (pp) REVERT: B 1 MET cc_start: 0.7226 (tmm) cc_final: 0.6669 (tmm) REVERT: B 32 HIS cc_start: 0.8879 (OUTLIER) cc_final: 0.8588 (m-70) REVERT: B 108 GLN cc_start: 0.7125 (tp-100) cc_final: 0.6689 (pt0) REVERT: B 310 ASN cc_start: 0.7339 (p0) cc_final: 0.7063 (p0) REVERT: B 356 MET cc_start: 0.9149 (tpp) cc_final: 0.8429 (tpt) REVERT: B 367 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: B 670 ARG cc_start: 0.6105 (ptm160) cc_final: 0.5612 (mtp180) REVERT: B 694 GLN cc_start: 0.8051 (mt0) cc_final: 0.7795 (mt0) REVERT: C 51 MET cc_start: 0.8203 (mmm) cc_final: 0.7828 (mmp) REVERT: C 146 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7109 (t0) REVERT: C 217 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8877 (m-80) REVERT: C 364 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.7144 (m-40) REVERT: C 458 MET cc_start: 0.3829 (mmm) cc_final: 0.3129 (mtp) REVERT: C 476 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5775 (ttp) REVERT: C 522 GLN cc_start: 0.7467 (tp40) cc_final: 0.7264 (tp-100) REVERT: C 630 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6403 (mmm160) REVERT: C 663 ASN cc_start: 0.8192 (t0) cc_final: 0.7949 (t0) REVERT: C 679 ILE cc_start: 0.4393 (OUTLIER) cc_final: 0.4103 (mt) outliers start: 115 outliers final: 83 residues processed: 362 average time/residue: 0.3459 time to fit residues: 185.1978 Evaluate side-chains 364 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 266 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 0.9990 chunk 192 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 213 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19053 Z= 0.149 Angle : 0.467 14.570 25924 Z= 0.239 Chirality : 0.039 0.145 2885 Planarity : 0.004 0.043 3163 Dihedral : 12.561 98.419 3154 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.23 % Allowed : 18.32 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.40 (0.18), residues: 2178 helix: 0.85 (0.17), residues: 949 sheet: -0.52 (0.32), residues: 239 loop : -1.29 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 188 HIS 0.003 0.001 HIS C 437 PHE 0.014 0.001 PHE C 330 TYR 0.009 0.001 TYR A 645 ARG 0.013 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 291 time to evaluate : 2.014 Fit side-chains revert: symmetry clash REVERT: A 189 ASP cc_start: 0.6237 (OUTLIER) cc_final: 0.5896 (p0) REVERT: A 315 TRP cc_start: 0.7425 (OUTLIER) cc_final: 0.6867 (p90) REVERT: A 384 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.5932 (t0) REVERT: A 474 GLU cc_start: 0.7713 (mp0) cc_final: 0.7433 (mp0) REVERT: A 616 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8456 (pp) REVERT: B 1 MET cc_start: 0.7266 (tmm) cc_final: 0.7042 (tmm) REVERT: B 32 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.8500 (m-70) REVERT: B 108 GLN cc_start: 0.6938 (tp-100) cc_final: 0.6580 (pt0) REVERT: B 310 ASN cc_start: 0.7238 (p0) cc_final: 0.6966 (p0) REVERT: B 670 ARG cc_start: 0.5954 (ptm160) cc_final: 0.5556 (mtp180) REVERT: B 694 GLN cc_start: 0.7946 (mt0) cc_final: 0.7642 (mt0) REVERT: C 51 MET cc_start: 0.8039 (mmm) cc_final: 0.7729 (mmp) REVERT: C 146 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7018 (t0) REVERT: C 217 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8811 (m-80) REVERT: C 364 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.7121 (m-40) REVERT: C 458 MET cc_start: 0.3727 (mmm) cc_final: 0.3075 (mtp) REVERT: C 476 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5768 (ttp) REVERT: C 522 GLN cc_start: 0.7401 (tp40) cc_final: 0.7181 (tp-100) REVERT: C 679 ILE cc_start: 0.4385 (OUTLIER) cc_final: 0.4085 (mt) outliers start: 82 outliers final: 59 residues processed: 347 average time/residue: 0.3428 time to fit residues: 174.7752 Evaluate side-chains 341 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 272 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 121 optimal weight: 0.0010 chunk 156 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 129 optimal weight: 0.0770 chunk 98 optimal weight: 5.9990 overall best weight: 1.3748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN C 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19053 Z= 0.158 Angle : 0.472 14.231 25924 Z= 0.241 Chirality : 0.039 0.145 2885 Planarity : 0.003 0.042 3163 Dihedral : 12.307 96.792 3141 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.44 % Allowed : 18.47 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.19 (0.18), residues: 2178 helix: 1.01 (0.17), residues: 944 sheet: -0.48 (0.32), residues: 245 loop : -1.14 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 188 HIS 0.003 0.001 HIS C 437 PHE 0.013 0.001 PHE C 330 TYR 0.010 0.001 TYR B 497 ARG 0.011 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 278 time to evaluate : 2.238 Fit side-chains REVERT: A 61 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7535 (tp) REVERT: A 315 TRP cc_start: 0.7414 (OUTLIER) cc_final: 0.6856 (p90) REVERT: A 384 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6011 (t0) REVERT: A 447 GLN cc_start: 0.7872 (mt0) cc_final: 0.7659 (mt0) REVERT: A 474 GLU cc_start: 0.7675 (mp0) cc_final: 0.7380 (mp0) REVERT: A 506 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7622 (mt) REVERT: A 540 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7692 (pp) REVERT: A 616 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8452 (pp) REVERT: B 32 HIS cc_start: 0.8767 (OUTLIER) cc_final: 0.8492 (m-70) REVERT: B 108 GLN cc_start: 0.6927 (tp-100) cc_final: 0.6583 (pt0) REVERT: B 116 GLN cc_start: 0.7252 (mm-40) cc_final: 0.6781 (mm-40) REVERT: B 310 ASN cc_start: 0.7251 (p0) cc_final: 0.6974 (p0) REVERT: B 356 MET cc_start: 0.9144 (tpp) cc_final: 0.8293 (tpt) REVERT: B 670 ARG cc_start: 0.6014 (ptm160) cc_final: 0.5568 (mtp180) REVERT: B 694 GLN cc_start: 0.7946 (mt0) cc_final: 0.7643 (mt0) REVERT: C 51 MET cc_start: 0.8043 (mmm) cc_final: 0.7705 (mmp) REVERT: C 146 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7000 (t0) REVERT: C 217 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8809 (m-80) REVERT: C 292 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6427 (tm-30) REVERT: C 364 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.7110 (m-40) REVERT: C 458 MET cc_start: 0.3657 (mmm) cc_final: 0.3148 (mtp) REVERT: C 476 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5743 (ttp) REVERT: C 522 GLN cc_start: 0.7431 (tp40) cc_final: 0.7222 (tp-100) REVERT: C 603 MET cc_start: 0.7818 (ttt) cc_final: 0.7561 (ttt) REVERT: C 630 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6511 (tpt170) REVERT: C 679 ILE cc_start: 0.4415 (OUTLIER) cc_final: 0.4037 (mt) outliers start: 86 outliers final: 64 residues processed: 340 average time/residue: 0.3613 time to fit residues: 179.3941 Evaluate side-chains 354 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 276 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 338 GLN Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 732 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 chunk 167 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19053 Z= 0.131 Angle : 0.462 14.560 25924 Z= 0.233 Chirality : 0.038 0.176 2885 Planarity : 0.003 0.041 3163 Dihedral : 12.072 95.593 3135 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.66 % Allowed : 19.35 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.01 (0.18), residues: 2178 helix: 1.20 (0.17), residues: 942 sheet: -0.36 (0.33), residues: 233 loop : -1.08 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 188 HIS 0.003 0.001 HIS C 437 PHE 0.013 0.001 PHE C 330 TYR 0.009 0.001 TYR B 555 ARG 0.002 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 276 time to evaluate : 2.064 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4382 (mmm) cc_final: 0.4066 (tpt) REVERT: A 61 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7540 (tp) REVERT: A 384 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.5943 (t0) REVERT: A 447 GLN cc_start: 0.7778 (mt0) cc_final: 0.7546 (mt0) REVERT: A 474 GLU cc_start: 0.7615 (mp0) cc_final: 0.7259 (mp0) REVERT: A 506 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7602 (mt) REVERT: A 540 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7653 (pp) REVERT: A 616 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8394 (pp) REVERT: B 32 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8491 (m-70) REVERT: B 108 GLN cc_start: 0.6881 (tp-100) cc_final: 0.6557 (pt0) REVERT: B 116 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6657 (mm-40) REVERT: B 310 ASN cc_start: 0.7242 (p0) cc_final: 0.6964 (p0) REVERT: B 670 ARG cc_start: 0.5961 (ptm160) cc_final: 0.5523 (mtp180) REVERT: B 694 GLN cc_start: 0.7934 (mt0) cc_final: 0.7655 (mt0) REVERT: C 146 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.6992 (t0) REVERT: C 217 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8798 (m-80) REVERT: C 292 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6426 (tm-30) REVERT: C 364 ASN cc_start: 0.7374 (OUTLIER) cc_final: 0.7125 (m-40) REVERT: C 458 MET cc_start: 0.3615 (mmm) cc_final: 0.3093 (mtp) REVERT: C 476 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5650 (ttp) REVERT: C 522 GLN cc_start: 0.7398 (tp40) cc_final: 0.7173 (tp-100) REVERT: C 603 MET cc_start: 0.7843 (ttt) cc_final: 0.7619 (ttt) REVERT: C 679 ILE cc_start: 0.4348 (OUTLIER) cc_final: 0.3946 (mt) REVERT: C 735 MET cc_start: 0.6424 (tmm) cc_final: 0.6008 (tmm) outliers start: 71 outliers final: 51 residues processed: 322 average time/residue: 0.3581 time to fit residues: 167.0053 Evaluate side-chains 331 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 268 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 8.9990 chunk 186 optimal weight: 0.2980 chunk 198 optimal weight: 7.9990 chunk 119 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 187 optimal weight: 0.6980 chunk 197 optimal weight: 0.0670 chunk 130 optimal weight: 0.0030 overall best weight: 0.3128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN C 348 ASN C 657 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19053 Z= 0.103 Angle : 0.448 14.584 25924 Z= 0.225 Chirality : 0.038 0.202 2885 Planarity : 0.003 0.042 3163 Dihedral : 11.772 93.518 3123 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.58 % Allowed : 20.43 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.21 (0.18), residues: 2178 helix: 1.40 (0.17), residues: 946 sheet: -0.20 (0.34), residues: 233 loop : -1.01 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 188 HIS 0.002 0.000 HIS B 394 PHE 0.012 0.001 PHE C 330 TYR 0.009 0.001 TYR A 161 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 289 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4184 (mmm) cc_final: 0.3920 (tpt) REVERT: A 61 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7447 (tp) REVERT: A 113 LYS cc_start: 0.8079 (tptt) cc_final: 0.7708 (tttt) REVERT: A 249 MET cc_start: 0.8390 (ttp) cc_final: 0.8111 (ttm) REVERT: A 384 ASP cc_start: 0.6850 (p0) cc_final: 0.5884 (t0) REVERT: A 447 GLN cc_start: 0.7692 (mt0) cc_final: 0.7455 (mt0) REVERT: A 474 GLU cc_start: 0.7554 (mp0) cc_final: 0.7195 (mp0) REVERT: A 616 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8378 (pp) REVERT: A 711 LEU cc_start: 0.7993 (tt) cc_final: 0.7516 (mt) REVERT: B 108 GLN cc_start: 0.6919 (tp-100) cc_final: 0.6629 (pt0) REVERT: B 116 GLN cc_start: 0.6895 (mm-40) cc_final: 0.6458 (mm-40) REVERT: B 248 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6297 (tp) REVERT: B 310 ASN cc_start: 0.7203 (p0) cc_final: 0.6935 (p0) REVERT: B 356 MET cc_start: 0.9142 (tpp) cc_final: 0.8110 (tpt) REVERT: B 670 ARG cc_start: 0.5766 (ptm160) cc_final: 0.5373 (mtp180) REVERT: B 694 GLN cc_start: 0.7978 (mt0) cc_final: 0.7675 (mt0) REVERT: C 28 MET cc_start: 0.7858 (ttp) cc_final: 0.7607 (ttp) REVERT: C 217 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: C 364 ASN cc_start: 0.7244 (OUTLIER) cc_final: 0.7024 (m-40) REVERT: C 458 MET cc_start: 0.3628 (mmm) cc_final: 0.3108 (mtp) REVERT: C 603 MET cc_start: 0.7784 (ttt) cc_final: 0.7576 (ttt) REVERT: C 679 ILE cc_start: 0.4304 (OUTLIER) cc_final: 0.3890 (mt) REVERT: C 735 MET cc_start: 0.6352 (tmm) cc_final: 0.5919 (tmm) outliers start: 50 outliers final: 32 residues processed: 320 average time/residue: 0.3621 time to fit residues: 167.3504 Evaluate side-chains 314 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 276 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 ASN B 202 GLN C 429 ASN C 657 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19053 Z= 0.142 Angle : 0.478 14.394 25924 Z= 0.240 Chirality : 0.039 0.150 2885 Planarity : 0.003 0.042 3163 Dihedral : 11.637 108.790 3107 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.17 % Allowed : 20.74 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.22 (0.18), residues: 2178 helix: 1.42 (0.17), residues: 944 sheet: -0.22 (0.33), residues: 241 loop : -1.01 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 188 HIS 0.002 0.001 HIS A 360 PHE 0.012 0.001 PHE C 330 TYR 0.009 0.001 TYR B 497 ARG 0.003 0.000 ARG C 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 269 time to evaluate : 2.142 Fit side-chains REVERT: A 1 MET cc_start: 0.4290 (mmm) cc_final: 0.3957 (tpt) REVERT: A 61 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7435 (tp) REVERT: A 113 LYS cc_start: 0.8056 (tptt) cc_final: 0.7769 (tmtt) REVERT: A 249 MET cc_start: 0.8405 (ttp) cc_final: 0.8145 (ttm) REVERT: A 315 TRP cc_start: 0.7412 (OUTLIER) cc_final: 0.6864 (p90) REVERT: A 384 ASP cc_start: 0.6943 (p0) cc_final: 0.5978 (t0) REVERT: A 447 GLN cc_start: 0.7672 (mt0) cc_final: 0.7455 (mt0) REVERT: A 474 GLU cc_start: 0.7573 (mp0) cc_final: 0.7193 (mp0) REVERT: A 540 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7652 (pp) REVERT: A 616 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8480 (pp) REVERT: A 711 LEU cc_start: 0.8032 (tt) cc_final: 0.7528 (mt) REVERT: B 108 GLN cc_start: 0.6967 (tp-100) cc_final: 0.6607 (pt0) REVERT: B 116 GLN cc_start: 0.6969 (mm-40) cc_final: 0.6519 (mm-40) REVERT: B 310 ASN cc_start: 0.7200 (p0) cc_final: 0.6907 (p0) REVERT: B 356 MET cc_start: 0.9158 (tpp) cc_final: 0.8201 (tpt) REVERT: B 670 ARG cc_start: 0.5739 (ptm160) cc_final: 0.5370 (mtp180) REVERT: B 694 GLN cc_start: 0.8038 (mt0) cc_final: 0.7752 (mt0) REVERT: C 28 MET cc_start: 0.7979 (ttp) cc_final: 0.7717 (ttp) REVERT: C 217 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: C 364 ASN cc_start: 0.7292 (OUTLIER) cc_final: 0.7034 (m-40) REVERT: C 458 MET cc_start: 0.3546 (mmm) cc_final: 0.3082 (mtp) REVERT: C 603 MET cc_start: 0.7912 (ttt) cc_final: 0.7621 (ttt) REVERT: C 630 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6337 (tpt170) REVERT: C 679 ILE cc_start: 0.4343 (OUTLIER) cc_final: 0.3927 (mt) REVERT: C 735 MET cc_start: 0.6397 (tmm) cc_final: 0.6078 (tmm) outliers start: 42 outliers final: 34 residues processed: 297 average time/residue: 0.3768 time to fit residues: 163.5328 Evaluate side-chains 302 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 260 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 726 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 161 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 ASN ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.157655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.133838 restraints weight = 23530.813| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.39 r_work: 0.3284 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19053 Z= 0.240 Angle : 0.543 13.513 25924 Z= 0.272 Chirality : 0.041 0.152 2885 Planarity : 0.004 0.042 3163 Dihedral : 11.847 106.789 3107 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.15 % Allowed : 20.12 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.05 (0.18), residues: 2178 helix: 1.20 (0.17), residues: 947 sheet: -0.39 (0.31), residues: 268 loop : -1.01 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 188 HIS 0.004 0.001 HIS A 360 PHE 0.012 0.001 PHE C 357 TYR 0.012 0.001 TYR B 497 ARG 0.003 0.000 ARG B 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4627.50 seconds wall clock time: 84 minutes 31.39 seconds (5071.39 seconds total)