Starting phenix.real_space_refine on Wed May 8 22:25:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzr_34402/05_2024/8gzr_34402_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzr_34402/05_2024/8gzr_34402.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzr_34402/05_2024/8gzr_34402_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzr_34402/05_2024/8gzr_34402_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzr_34402/05_2024/8gzr_34402_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzr_34402/05_2024/8gzr_34402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzr_34402/05_2024/8gzr_34402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzr_34402/05_2024/8gzr_34402_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzr_34402/05_2024/8gzr_34402_updated.pdb" } resolution = 2.8 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= 0.005 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: 7 Type Number sf(0) Gaussians Mn 3 7.51 5 Zn 2 6.06 5 P 37 5.49 5 S 65 5.16 5 C 6993 2.51 5 N 2027 2.21 5 O 2191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A ARG 688": "NH1" <-> "NH2" Residue "A ASP 720": "OD1" <-> "OD2" Residue "A ASP 732": "OD1" <-> "OD2" Residue "A ARG 856": "NH1" <-> "NH2" Residue "A GLU 877": "OE1" <-> "OE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B ARG 525": "NH1" <-> "NH2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B ARG 539": "NH1" <-> "NH2" Residue "B ASP 542": "OD1" <-> "OD2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B ARG 618": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 11318 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 7057 Classifications: {'peptide': 880} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 40, 'TRANS': 839} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 3474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3474 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 26, 'TRANS': 416} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 706 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 18, 'rna3p_pyr': 12} Link IDs: {'rna2p': 3, 'rna3p': 29} Chain breaks: 1 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 55 Unusual residues: {' MN': 2, ' ZN': 2, 'CDP': 1} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MN': 1, 'CDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5788 SG CYS A 728 74.365 45.793 41.590 1.00 32.82 S ATOM 6763 SG CYS A 847 75.018 43.082 44.279 1.00 41.34 S ATOM 3533 SG CYS A 446 83.849 90.378 49.020 1.00 49.25 S ATOM 3549 SG CYS A 449 82.166 88.650 46.383 1.00 47.31 S Time building chain proxies: 6.34, per 1000 atoms: 0.56 Number of scatterers: 11318 At special positions: 0 Unit cell: (122.618, 108.533, 113.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Mn 3 24.99 S 65 16.00 P 37 15.00 O 2191 8.00 N 2027 7.00 C 6993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.66 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" NE2 HIS A 714 " pdb="ZN ZN A1003 " - pdb=" NE2 HIS A 712 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 728 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 847 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" NE2 HIS A 441 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 446 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 449 " Number of angles added : 2 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 13 sheets defined 39.2% alpha, 10.7% beta 10 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 removed outlier: 3.641A pdb=" N GLN A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 30 removed outlier: 4.369A pdb=" N LYS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 58 through 67 removed outlier: 3.575A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.947A pdb=" N GLY A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 154 through 171 removed outlier: 3.546A pdb=" N GLU A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 227 through 243 removed outlier: 3.627A pdb=" N PHE A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 329 through 333 removed outlier: 4.131A pdb=" N VAL A 333 " --> pdb=" O PRO A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 338 No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 395 through 401 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 429 through 443 removed outlier: 3.594A pdb=" N GLN A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 493 removed outlier: 5.663A pdb=" N PHE A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASN A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 511 through 522 removed outlier: 4.481A pdb=" N GLY A 515 " --> pdb=" O HIS A 512 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR A 516 " --> pdb=" O LYS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 543 through 555 removed outlier: 4.623A pdb=" N ILE A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N THR A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLN A 554 " --> pdb=" O GLU A 550 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLN A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 605 through 624 Processing helix chain 'A' and resid 630 through 633 No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 640 through 657 removed outlier: 6.464A pdb=" N VAL A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLU A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 749 through 765 removed outlier: 3.735A pdb=" N ALA A 752 " --> pdb=" O LYS A 749 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS A 753 " --> pdb=" O GLU A 750 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 754 " --> pdb=" O THR A 751 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET A 765 " --> pdb=" O TRP A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 781 Processing helix chain 'A' and resid 806 through 817 Processing helix chain 'A' and resid 841 through 846 Processing helix chain 'A' and resid 854 through 861 Processing helix chain 'A' and resid 863 through 874 Processing helix chain 'B' and resid 181 through 184 Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 226 through 235 Processing helix chain 'B' and resid 263 through 271 Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 350 through 353 No H-bonds generated for 'chain 'B' and resid 350 through 353' Processing helix chain 'B' and resid 366 through 379 removed outlier: 3.597A pdb=" N ASN B 379 " --> pdb=" O CYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 398 removed outlier: 4.978A pdb=" N GLN B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 452 through 461 removed outlier: 3.554A pdb=" N ARG B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 498 removed outlier: 3.672A pdb=" N ASN B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 513 No H-bonds generated for 'chain 'B' and resid 511 through 513' Processing helix chain 'B' and resid 517 through 520 No H-bonds generated for 'chain 'B' and resid 517 through 520' Processing helix chain 'B' and resid 528 through 539 Processing helix chain 'B' and resid 545 through 554 removed outlier: 3.795A pdb=" N GLU B 554 " --> pdb=" O LYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 564 No H-bonds generated for 'chain 'B' and resid 562 through 564' Processing helix chain 'B' and resid 599 through 601 No H-bonds generated for 'chain 'B' and resid 599 through 601' Processing helix chain 'B' and resid 605 through 615 Processing sheet with id= A, first strand: chain 'A' and resid 34 through 36 removed outlier: 5.743A pdb=" N THR A 250 " --> pdb=" O GLU A 35 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 203 through 205 removed outlier: 7.322A pdb=" N VAL A 77 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A 100 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASP A 79 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY A 102 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 740 through 742 removed outlier: 6.768A pdb=" N GLY A 745 " --> pdb=" O ILE A 320 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 340 through 342 Processing sheet with id= E, first strand: chain 'A' and resid 451 through 455 Processing sheet with id= F, first strand: chain 'A' and resid 575 through 583 removed outlier: 3.744A pdb=" N GLY A 306 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER A 593 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR A 304 " --> pdb=" O SER A 593 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 658 through 661 Processing sheet with id= H, first strand: chain 'A' and resid 712 through 717 Processing sheet with id= I, first strand: chain 'A' and resid 787 through 789 Processing sheet with id= J, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.626A pdb=" N ALA B 312 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N MET B 192 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE B 314 " --> pdb=" O MET B 192 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 333 through 336 removed outlier: 6.933A pdb=" N ASP B 471 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLU B 336 " --> pdb=" O ASP B 471 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR B 473 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 431 through 435 removed outlier: 3.694A pdb=" N LYS B 431 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 581 through 583 359 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 5.05 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: 1806 1.31 - 1.45: 3380 1.45 - 1.58: 6280 1.58 - 1.72: 72 1.72 - 1.85: 112 Bond restraints: 11650 Sorted by residual: bond pdb=" C8 SAH A1005 " pdb=" N9 SAH A1005 " ideal model delta sigma weight residual 1.370 1.413 -0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" C4 SAH A1005 " pdb=" N3 SAH A1005 " ideal model delta sigma weight residual 1.330 1.372 -0.042 2.00e-02 2.50e+03 4.38e+00 bond pdb=" CA SAH A1005 " pdb=" C SAH A1005 " ideal model delta sigma weight residual 1.525 1.568 -0.043 2.10e-02 2.27e+03 4.22e+00 bond pdb=" C1' SAH A1005 " pdb=" N9 SAH A1005 " ideal model delta sigma weight residual 1.440 1.480 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" C8 SAH A1005 " pdb=" N7 SAH A1005 " ideal model delta sigma weight residual 1.299 1.337 -0.038 2.00e-02 2.50e+03 3.55e+00 ... (remaining 11645 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.11: 474 106.11 - 113.12: 6385 113.12 - 120.13: 4153 120.13 - 127.13: 4679 127.13 - 134.14: 253 Bond angle restraints: 15944 Sorted by residual: angle pdb=" C1' SAH A1005 " pdb=" C2' SAH A1005 " pdb=" O2' SAH A1005 " ideal model delta sigma weight residual 114.27 106.21 8.06 3.00e+00 1.11e-01 7.23e+00 angle pdb=" CA ARG A 729 " pdb=" C ARG A 729 " pdb=" N PRO A 730 " ideal model delta sigma weight residual 117.68 119.44 -1.76 7.10e-01 1.98e+00 6.16e+00 angle pdb=" OG1 THR B 476 " pdb=" CB THR B 476 " pdb=" CG2 THR B 476 " ideal model delta sigma weight residual 109.30 104.65 4.65 2.00e+00 2.50e-01 5.40e+00 angle pdb=" CG SAH A1005 " pdb=" SD SAH A1005 " pdb=" C5' SAH A1005 " ideal model delta sigma weight residual 101.77 108.61 -6.84 3.00e+00 1.11e-01 5.19e+00 angle pdb=" C SER A 502 " pdb=" N TYR A 503 " pdb=" CA TYR A 503 " ideal model delta sigma weight residual 121.54 125.67 -4.13 1.91e+00 2.74e-01 4.68e+00 ... (remaining 15939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.72: 6535 24.72 - 49.45: 396 49.45 - 74.17: 73 74.17 - 98.90: 5 98.90 - 123.62: 1 Dihedral angle restraints: 7010 sinusoidal: 3197 harmonic: 3813 Sorted by residual: dihedral pdb=" CA TYR A 451 " pdb=" C TYR A 451 " pdb=" N ASN A 452 " pdb=" CA ASN A 452 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA HIS A 711 " pdb=" C HIS A 711 " pdb=" N HIS A 712 " pdb=" CA HIS A 712 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LYS A 357 " pdb=" C LYS A 357 " pdb=" N VAL A 358 " pdb=" CA VAL A 358 " ideal model delta harmonic sigma weight residual 180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 7007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1558 0.065 - 0.129: 185 0.129 - 0.194: 4 0.194 - 0.259: 0 0.259 - 0.323: 1 Chirality restraints: 1748 Sorted by residual: chirality pdb=" C2' SAH A1005 " pdb=" C1' SAH A1005 " pdb=" C3' SAH A1005 " pdb=" O2' SAH A1005 " both_signs ideal model delta sigma weight residual False -2.53 -2.85 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB VAL B 462 " pdb=" CA VAL B 462 " pdb=" CG1 VAL B 462 " pdb=" CG2 VAL B 462 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" C1' SAH A1005 " pdb=" C2' SAH A1005 " pdb=" N9 SAH A1005 " pdb=" O4' SAH A1005 " both_signs ideal model delta sigma weight residual False 2.35 2.52 -0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 1745 not shown) Planarity restraints: 1919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 289 " -0.017 2.00e-02 2.50e+03 1.59e-02 4.42e+00 pdb=" CG PHE B 289 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 289 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 289 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 289 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 289 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 474 " -0.000 2.00e-02 2.50e+03 1.27e-02 4.04e+00 pdb=" CG TRP A 474 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 474 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 474 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 474 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 474 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 474 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 474 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 474 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 729 " -0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 730 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 730 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 730 " -0.026 5.00e-02 4.00e+02 ... (remaining 1916 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 22 2.37 - 3.00: 5800 3.00 - 3.63: 16879 3.63 - 4.27: 28854 4.27 - 4.90: 45893 Nonbonded interactions: 97448 Sorted by model distance: nonbonded pdb="MN MN A1001 " pdb=" O2B CDP A1006 " model vdw 1.733 2.320 nonbonded pdb=" OD1 ASP A 533 " pdb="MN MN A1001 " model vdw 1.792 2.320 nonbonded pdb=" OD2 ASP A 533 " pdb="MN MN A1002 " model vdw 1.834 2.320 nonbonded pdb="MN MN B 701 " pdb=" O1B CDP B 702 " model vdw 1.836 2.320 nonbonded pdb=" OD2 ASP A 663 " pdb="MN MN A1001 " model vdw 1.897 2.320 ... (remaining 97443 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.550 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 36.830 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11650 Z= 0.265 Angle : 0.551 8.064 15944 Z= 0.311 Chirality : 0.042 0.323 1748 Planarity : 0.004 0.046 1919 Dihedral : 15.366 123.622 4552 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1319 helix: 0.61 (0.22), residues: 535 sheet: -0.87 (0.37), residues: 170 loop : -0.18 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 474 HIS 0.004 0.001 HIS B 488 PHE 0.036 0.002 PHE B 289 TYR 0.016 0.001 TYR A 482 ARG 0.002 0.000 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.470 Fit side-chains REVERT: A 39 THR cc_start: 0.8356 (p) cc_final: 0.8129 (p) REVERT: A 141 ASP cc_start: 0.8450 (m-30) cc_final: 0.8028 (m-30) REVERT: A 240 ASN cc_start: 0.8408 (t0) cc_final: 0.7935 (t0) REVERT: A 356 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7175 (mt-10) REVERT: B 336 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7195 (tt0) REVERT: B 421 ASP cc_start: 0.7627 (m-30) cc_final: 0.7400 (m-30) REVERT: B 619 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7922 (ttmt) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 1.7825 time to fit residues: 305.5117 Evaluate side-chains 133 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 102 optimal weight: 0.0010 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 122 optimal weight: 0.0980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 742 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11650 Z= 0.115 Angle : 0.424 5.232 15944 Z= 0.224 Chirality : 0.038 0.141 1748 Planarity : 0.004 0.044 1919 Dihedral : 12.003 116.918 1960 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.89 % Allowed : 6.08 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1319 helix: 1.04 (0.23), residues: 538 sheet: -0.64 (0.40), residues: 160 loop : 0.01 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 171 HIS 0.002 0.001 HIS B 195 PHE 0.019 0.001 PHE B 289 TYR 0.011 0.001 TYR A 482 ARG 0.004 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.319 Fit side-chains REVERT: A 141 ASP cc_start: 0.8411 (m-30) cc_final: 0.8034 (m-30) REVERT: A 240 ASN cc_start: 0.8364 (t0) cc_final: 0.7987 (t0) REVERT: A 356 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7132 (mt-10) REVERT: B 336 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7292 (mt-10) REVERT: B 378 LYS cc_start: 0.7857 (mtpm) cc_final: 0.7486 (mtpt) REVERT: B 421 ASP cc_start: 0.7561 (m-30) cc_final: 0.7358 (m-30) outliers start: 10 outliers final: 2 residues processed: 149 average time/residue: 1.6684 time to fit residues: 264.9315 Evaluate side-chains 132 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain B residue 408 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 98 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11650 Z= 0.147 Angle : 0.430 5.441 15944 Z= 0.225 Chirality : 0.039 0.134 1748 Planarity : 0.004 0.046 1919 Dihedral : 11.979 119.077 1960 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.72 % Allowed : 8.32 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1319 helix: 1.17 (0.23), residues: 536 sheet: -0.49 (0.39), residues: 170 loop : 0.08 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 859 HIS 0.003 0.001 HIS B 488 PHE 0.017 0.001 PHE B 289 TYR 0.014 0.001 TYR A 482 ARG 0.003 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.387 Fit side-chains REVERT: A 141 ASP cc_start: 0.8446 (m-30) cc_final: 0.8065 (m-30) REVERT: A 240 ASN cc_start: 0.8406 (t0) cc_final: 0.8037 (t0) REVERT: A 356 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7156 (mt-10) REVERT: B 378 LYS cc_start: 0.7813 (mtpm) cc_final: 0.7487 (mtpt) outliers start: 8 outliers final: 5 residues processed: 144 average time/residue: 1.6040 time to fit residues: 246.4492 Evaluate side-chains 138 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 408 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11650 Z= 0.236 Angle : 0.477 5.899 15944 Z= 0.249 Chirality : 0.041 0.142 1748 Planarity : 0.004 0.046 1919 Dihedral : 12.113 124.834 1960 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.61 % Allowed : 8.14 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1319 helix: 1.08 (0.23), residues: 535 sheet: -0.49 (0.39), residues: 170 loop : 0.07 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 859 HIS 0.004 0.001 HIS B 488 PHE 0.018 0.002 PHE A 674 TYR 0.019 0.001 TYR A 482 ARG 0.003 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 1.253 Fit side-chains REVERT: A 141 ASP cc_start: 0.8443 (m-30) cc_final: 0.8043 (m-30) REVERT: A 240 ASN cc_start: 0.8457 (t0) cc_final: 0.8093 (t0) REVERT: A 253 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8113 (pttp) REVERT: A 356 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7241 (mt-10) REVERT: A 824 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7965 (ttp) REVERT: B 378 LYS cc_start: 0.7773 (mtpm) cc_final: 0.7472 (mtpt) REVERT: B 382 LYS cc_start: 0.7792 (ptpt) cc_final: 0.7500 (pttp) outliers start: 18 outliers final: 10 residues processed: 150 average time/residue: 1.6706 time to fit residues: 266.8539 Evaluate side-chains 146 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 0.0770 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11650 Z= 0.203 Angle : 0.461 5.977 15944 Z= 0.241 Chirality : 0.040 0.144 1748 Planarity : 0.004 0.046 1919 Dihedral : 12.071 123.341 1960 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.70 % Allowed : 9.21 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1319 helix: 1.09 (0.23), residues: 534 sheet: -0.45 (0.40), residues: 160 loop : 0.10 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 583 HIS 0.004 0.001 HIS B 488 PHE 0.016 0.001 PHE A 674 TYR 0.017 0.001 TYR A 482 ARG 0.002 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.495 Fit side-chains REVERT: A 141 ASP cc_start: 0.8448 (m-30) cc_final: 0.8059 (m-30) REVERT: A 240 ASN cc_start: 0.8456 (t0) cc_final: 0.8101 (t0) REVERT: A 356 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7238 (mt-10) REVERT: A 824 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7954 (ttp) REVERT: B 378 LYS cc_start: 0.7787 (mtpm) cc_final: 0.7511 (mtpt) REVERT: B 382 LYS cc_start: 0.7790 (ptpt) cc_final: 0.7485 (pttp) REVERT: B 581 GLU cc_start: 0.8018 (tt0) cc_final: 0.7657 (tt0) outliers start: 19 outliers final: 9 residues processed: 146 average time/residue: 1.7350 time to fit residues: 269.6497 Evaluate side-chains 144 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.0980 chunk 117 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 chunk 130 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 613 ASN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11650 Z= 0.138 Angle : 0.425 5.544 15944 Z= 0.222 Chirality : 0.038 0.137 1748 Planarity : 0.004 0.045 1919 Dihedral : 11.957 119.827 1960 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.34 % Allowed : 9.75 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1319 helix: 1.25 (0.23), residues: 534 sheet: -0.33 (0.40), residues: 165 loop : 0.15 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 583 HIS 0.003 0.001 HIS B 488 PHE 0.014 0.001 PHE B 534 TYR 0.013 0.001 TYR A 482 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.290 Fit side-chains REVERT: A 141 ASP cc_start: 0.8450 (m-30) cc_final: 0.8088 (m-30) REVERT: A 240 ASN cc_start: 0.8440 (t0) cc_final: 0.8085 (t0) REVERT: A 356 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7212 (mt-10) REVERT: B 378 LYS cc_start: 0.7737 (mtpm) cc_final: 0.7470 (mtpt) REVERT: B 382 LYS cc_start: 0.7761 (ptpt) cc_final: 0.7443 (pttp) outliers start: 15 outliers final: 7 residues processed: 150 average time/residue: 1.6559 time to fit residues: 264.8165 Evaluate side-chains 144 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 408 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 79 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11650 Z= 0.212 Angle : 0.462 5.870 15944 Z= 0.241 Chirality : 0.040 0.138 1748 Planarity : 0.004 0.046 1919 Dihedral : 12.034 122.965 1960 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.52 % Allowed : 10.02 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.23), residues: 1319 helix: 1.18 (0.23), residues: 535 sheet: -0.44 (0.39), residues: 170 loop : 0.15 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 859 HIS 0.004 0.001 HIS B 488 PHE 0.017 0.002 PHE A 674 TYR 0.017 0.001 TYR A 482 ARG 0.002 0.000 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.228 Fit side-chains REVERT: A 141 ASP cc_start: 0.8467 (m-30) cc_final: 0.8088 (m-30) REVERT: A 240 ASN cc_start: 0.8461 (t0) cc_final: 0.8084 (t0) REVERT: A 352 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7535 (ttp-170) REVERT: A 356 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7210 (mt-10) REVERT: A 824 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7968 (ttp) REVERT: B 378 LYS cc_start: 0.7775 (mtpm) cc_final: 0.7516 (mtpt) REVERT: B 382 LYS cc_start: 0.7763 (ptpt) cc_final: 0.7450 (pttp) outliers start: 17 outliers final: 10 residues processed: 150 average time/residue: 1.7568 time to fit residues: 279.8177 Evaluate side-chains 149 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 82 optimal weight: 0.0980 chunk 88 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 0.0470 chunk 124 optimal weight: 0.8980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11650 Z= 0.114 Angle : 0.412 5.057 15944 Z= 0.216 Chirality : 0.038 0.129 1748 Planarity : 0.004 0.045 1919 Dihedral : 11.873 117.929 1960 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.72 % Allowed : 11.27 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1319 helix: 1.38 (0.23), residues: 535 sheet: -0.31 (0.40), residues: 165 loop : 0.17 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 583 HIS 0.003 0.000 HIS B 488 PHE 0.014 0.001 PHE B 534 TYR 0.010 0.001 TYR A 482 ARG 0.002 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 1.442 Fit side-chains REVERT: A 141 ASP cc_start: 0.8430 (m-30) cc_final: 0.8088 (m-30) REVERT: A 240 ASN cc_start: 0.8427 (t0) cc_final: 0.8081 (t0) REVERT: A 321 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8503 (m-40) REVERT: B 378 LYS cc_start: 0.7720 (mtpm) cc_final: 0.7477 (mtpt) REVERT: B 382 LYS cc_start: 0.7732 (ptpt) cc_final: 0.7415 (pttp) REVERT: B 581 GLU cc_start: 0.7935 (tt0) cc_final: 0.7557 (tt0) outliers start: 8 outliers final: 4 residues processed: 152 average time/residue: 1.6179 time to fit residues: 262.9259 Evaluate side-chains 142 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 408 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.7980 chunk 121 optimal weight: 0.2980 chunk 124 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 95 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 79 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 742 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11650 Z= 0.121 Angle : 0.420 5.105 15944 Z= 0.220 Chirality : 0.038 0.172 1748 Planarity : 0.004 0.045 1919 Dihedral : 11.855 117.985 1960 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.98 % Allowed : 11.90 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1319 helix: 1.45 (0.23), residues: 535 sheet: -0.30 (0.40), residues: 165 loop : 0.19 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 583 HIS 0.003 0.001 HIS B 488 PHE 0.016 0.001 PHE B 534 TYR 0.011 0.001 TYR A 482 ARG 0.002 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.573 Fit side-chains REVERT: A 141 ASP cc_start: 0.8438 (m-30) cc_final: 0.8089 (m-30) REVERT: A 240 ASN cc_start: 0.8427 (t0) cc_final: 0.8059 (t0) REVERT: B 339 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7763 (t70) REVERT: B 378 LYS cc_start: 0.7752 (mtpm) cc_final: 0.7505 (mtpt) REVERT: B 382 LYS cc_start: 0.7691 (ptpt) cc_final: 0.7370 (pttp) REVERT: B 581 GLU cc_start: 0.7954 (tt0) cc_final: 0.7571 (tt0) outliers start: 11 outliers final: 4 residues processed: 144 average time/residue: 1.6129 time to fit residues: 247.8369 Evaluate side-chains 144 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 408 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 0.0970 chunk 134 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 85 optimal weight: 0.2980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 742 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11650 Z= 0.120 Angle : 0.417 4.952 15944 Z= 0.219 Chirality : 0.038 0.172 1748 Planarity : 0.004 0.045 1919 Dihedral : 11.828 117.953 1960 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.89 % Allowed : 12.43 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1319 helix: 1.47 (0.23), residues: 539 sheet: -0.26 (0.40), residues: 165 loop : 0.20 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 583 HIS 0.003 0.001 HIS B 488 PHE 0.013 0.001 PHE B 534 TYR 0.011 0.001 TYR A 482 ARG 0.003 0.000 ARG A 352 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 1.386 Fit side-chains REVERT: A 141 ASP cc_start: 0.8436 (m-30) cc_final: 0.8107 (m-30) REVERT: A 240 ASN cc_start: 0.8428 (t0) cc_final: 0.8082 (t0) REVERT: B 339 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7380 (t70) REVERT: B 378 LYS cc_start: 0.7739 (mtpm) cc_final: 0.7501 (mtpt) REVERT: B 581 GLU cc_start: 0.7877 (tt0) cc_final: 0.7523 (tt0) outliers start: 10 outliers final: 5 residues processed: 150 average time/residue: 1.5906 time to fit residues: 254.9298 Evaluate side-chains 146 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 408 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 110 optimal weight: 0.1980 chunk 13 optimal weight: 0.0370 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 321 ASN A 742 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.087522 restraints weight = 13288.249| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.62 r_work: 0.2700 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11650 Z= 0.113 Angle : 0.414 4.923 15944 Z= 0.217 Chirality : 0.038 0.153 1748 Planarity : 0.004 0.045 1919 Dihedral : 11.782 117.061 1960 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.81 % Allowed : 12.70 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.23), residues: 1319 helix: 1.53 (0.23), residues: 539 sheet: -0.24 (0.40), residues: 165 loop : 0.24 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 583 HIS 0.003 0.000 HIS B 488 PHE 0.013 0.001 PHE B 534 TYR 0.010 0.001 TYR A 482 ARG 0.002 0.000 ARG A 352 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -oh -his -flip -keep -allalt -limit120 -pen9999 -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: