Starting phenix.real_space_refine on Wed Feb 4 10:09:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lwq_63456/02_2026/9lwq_63456_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lwq_63456/02_2026/9lwq_63456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lwq_63456/02_2026/9lwq_63456_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lwq_63456/02_2026/9lwq_63456_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lwq_63456/02_2026/9lwq_63456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lwq_63456/02_2026/9lwq_63456.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.047 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: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 6262 2.51 5 N 1696 2.21 5 O 1785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9810 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7830 Classifications: {'peptide': 971} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 925} Chain breaks: 5 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1946 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 231} Chain breaks: 4 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'QIH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.26, per 1000 atoms: 0.23 Number of scatterers: 9810 At special positions: 0 Unit cell: (89.964, 125.307, 112.455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1785 8.00 N 1696 7.00 C 6262 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 - 3.00 Amino acid : True - 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: 0.75 Conformation dependent library (CDL) restraints added in 465.4 milliseconds 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2314 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 11 sheets defined 52.3% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.739A pdb=" N ARG A 54 " --> pdb=" O PHE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.632A pdb=" N TYR A 68 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 removed outlier: 4.060A pdb=" N ARG A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.653A pdb=" N ASP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 4.212A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 496 removed outlier: 3.513A pdb=" N GLU A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 536 removed outlier: 4.538A pdb=" N GLN A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.561A pdb=" N VAL A 559 " --> pdb=" O HIS A 556 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 629 Processing helix chain 'A' and resid 632 through 641 removed outlier: 4.030A pdb=" N LYS A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR A 641 " --> pdb=" O GLN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 659 Processing helix chain 'A' and resid 660 through 675 removed outlier: 3.918A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 679 No H-bonds generated for 'chain 'A' and resid 677 through 679' Processing helix chain 'A' and resid 680 through 695 removed outlier: 3.525A pdb=" N PHE A 684 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 721 removed outlier: 4.020A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 removed outlier: 3.588A pdb=" N GLN A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.532A pdb=" N GLN A 749 " --> pdb=" O MET A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 removed outlier: 4.351A pdb=" N LEU A 793 " --> pdb=" O MET A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 863 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 886 through 888 No H-bonds generated for 'chain 'A' and resid 886 through 888' Processing helix chain 'A' and resid 889 through 911 removed outlier: 3.578A pdb=" N PHE A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 919 No H-bonds generated for 'chain 'A' and resid 917 through 919' Processing helix chain 'A' and resid 957 through 965 Processing helix chain 'A' and resid 970 through 973 Processing helix chain 'A' and resid 974 through 993 Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.938A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 4.027A pdb=" N ILE A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A1022 " --> pdb=" O ASP A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1047 Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 442 through 509 removed outlier: 4.307A pdb=" N LYS B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 523 Processing helix chain 'B' and resid 523 through 582 removed outlier: 3.576A pdb=" N TYR B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 566 " --> pdb=" O ARG B 562 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS B 567 " --> pdb=" O MET B 563 " (cutoff:3.500A) Proline residue: B 568 - end of helix removed outlier: 3.623A pdb=" N GLN B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 573 " --> pdb=" O ASP B 569 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.943A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 212 removed outlier: 8.178A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 287 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TRP A 195 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ALA A 289 " --> pdb=" O TRP A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.548A pdb=" N LYS A 485 " --> pdb=" O LYS A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.759A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE A 338 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU A 476 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS A 340 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 371 removed outlier: 3.682A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE A 360 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP A 369 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR A 358 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 371 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 356 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 371 removed outlier: 3.682A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE A 360 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP A 369 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR A 358 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 371 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 356 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AA8, first strand: chain 'A' and resid 770 through 771 removed outlier: 3.591A pdb=" N ARG A 770 " --> pdb=" O TRP A 780 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AB1, first strand: chain 'B' and resid 355 through 358 Processing sheet with id=AB2, first strand: chain 'B' and resid 384 through 386 494 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 1637 1.29 - 1.42: 2542 1.42 - 1.55: 5732 1.55 - 1.68: 0 1.68 - 1.81: 105 Bond restraints: 10016 Sorted by residual: bond pdb=" C2 QIH A1101 " pdb=" N1 QIH A1101 " ideal model delta sigma weight residual 1.462 1.291 0.171 2.00e-02 2.50e+03 7.28e+01 bond pdb=" C18 QIH A1101 " pdb=" N5 QIH A1101 " ideal model delta sigma weight residual 1.356 1.496 -0.140 2.00e-02 2.50e+03 4.88e+01 bond pdb=" C11 QIH A1101 " pdb=" N4 QIH A1101 " ideal model delta sigma weight residual 1.373 1.495 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C5 QIH A1101 " pdb=" N2 QIH A1101 " ideal model delta sigma weight residual 1.374 1.487 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" C PRO A 471 " pdb=" O PRO A 471 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.30e-02 5.92e+03 2.91e+01 ... (remaining 10011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 13340 2.27 - 4.54: 168 4.54 - 6.81: 17 6.81 - 9.08: 1 9.08 - 11.35: 3 Bond angle restraints: 13529 Sorted by residual: angle pdb=" C PRO A 471 " pdb=" CA PRO A 471 " pdb=" CB PRO A 471 " ideal model delta sigma weight residual 111.56 100.21 11.35 1.65e+00 3.67e-01 4.73e+01 angle pdb=" C PRO A 57 " pdb=" CA PRO A 57 " pdb=" CB PRO A 57 " ideal model delta sigma weight residual 111.56 100.89 10.67 1.65e+00 3.67e-01 4.18e+01 angle pdb=" CA ALA A 496 " pdb=" C ALA A 496 " pdb=" O ALA A 496 " ideal model delta sigma weight residual 121.19 114.91 6.28 1.10e+00 8.26e-01 3.26e+01 angle pdb=" N TYR B 504 " pdb=" CA TYR B 504 " pdb=" C TYR B 504 " ideal model delta sigma weight residual 111.69 117.72 -6.03 1.23e+00 6.61e-01 2.41e+01 angle pdb=" N GLU A 494 " pdb=" CA GLU A 494 " pdb=" C GLU A 494 " ideal model delta sigma weight residual 113.55 107.55 6.00 1.26e+00 6.30e-01 2.27e+01 ... (remaining 13524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 5943 35.06 - 70.12: 147 70.12 - 105.18: 15 105.18 - 140.24: 5 140.24 - 175.30: 4 Dihedral angle restraints: 6114 sinusoidal: 2557 harmonic: 3557 Sorted by residual: dihedral pdb=" CD ARG A 230 " pdb=" NE ARG A 230 " pdb=" CZ ARG A 230 " pdb=" NH1 ARG A 230 " ideal model delta sinusoidal sigma weight residual 0.00 63.19 -63.19 1 1.00e+01 1.00e-02 5.27e+01 dihedral pdb=" C PRO A 471 " pdb=" N PRO A 471 " pdb=" CA PRO A 471 " pdb=" CB PRO A 471 " ideal model delta harmonic sigma weight residual -120.70 -108.95 -11.75 0 2.50e+00 1.60e-01 2.21e+01 dihedral pdb=" C24 QIH A1101 " pdb=" C8 QIH A1101 " pdb=" N3 QIH A1101 " pdb=" C9 QIH A1101 " ideal model delta sinusoidal sigma weight residual -60.45 114.85 -175.30 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 6111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1207 0.050 - 0.100: 221 0.100 - 0.151: 42 0.151 - 0.201: 5 0.201 - 0.251: 4 Chirality restraints: 1479 Sorted by residual: chirality pdb=" CA HIS A 495 " pdb=" N HIS A 495 " pdb=" C HIS A 495 " pdb=" CB HIS A 495 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA ALA A 496 " pdb=" N ALA A 496 " pdb=" C ALA A 496 " pdb=" CB ALA A 496 " both_signs ideal model delta sigma weight residual False 2.48 2.71 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LEU A 473 " pdb=" N LEU A 473 " pdb=" C LEU A 473 " pdb=" CB LEU A 473 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1476 not shown) Planarity restraints: 1735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 230 " 0.986 9.50e-02 1.11e+02 4.42e-01 1.18e+02 pdb=" NE ARG A 230 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 230 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 230 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 230 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 471 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C PRO A 471 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO A 471 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 472 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 56 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C TYR A 56 " -0.027 2.00e-02 2.50e+03 pdb=" O TYR A 56 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO A 57 " 0.009 2.00e-02 2.50e+03 ... (remaining 1732 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 93 2.58 - 3.16: 8666 3.16 - 3.74: 14869 3.74 - 4.32: 20851 4.32 - 4.90: 34952 Nonbonded interactions: 79431 Sorted by model distance: nonbonded pdb=" OG1 THR A 358 " pdb=" OH TYR A 389 " model vdw 1.999 3.040 nonbonded pdb=" OH TYR A 836 " pdb=" O ILE A 932 " model vdw 2.001 3.040 nonbonded pdb=" N GLY A 804 " pdb=" O CYS A 844 " model vdw 2.136 3.120 nonbonded pdb=" OD1 ASN B 517 " pdb=" N GLU B 518 " model vdw 2.166 3.120 nonbonded pdb=" OD1 ASN A 444 " pdb=" NZ LYS A 468 " model vdw 2.178 3.120 ... (remaining 79426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.170 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.005 0.171 10016 Z= 0.275 Angle : 0.599 11.346 13529 Z= 0.352 Chirality : 0.042 0.251 1479 Planarity : 0.011 0.442 1735 Dihedral : 17.068 175.297 3800 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 34.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.18 % Favored : 92.48 % Rotamer: Outliers : 1.32 % Allowed : 0.57 % Favored : 98.11 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.26), residues: 1184 helix: 1.41 (0.22), residues: 574 sheet: -1.36 (0.41), residues: 149 loop : -0.98 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 401 TYR 0.014 0.001 TYR A 904 PHE 0.014 0.001 PHE A 937 TRP 0.013 0.001 TRP A 780 HIS 0.009 0.001 HIS A1047 Details of bonding type rmsd covalent geometry : bond 0.00533 (10016) covalent geometry : angle 0.59909 (13529) hydrogen bonds : bond 0.14710 ( 492) hydrogen bonds : angle 5.86080 ( 1422) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.407 Fit side-chains REVERT: A 230 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6225 (ttm110) outliers start: 14 outliers final: 3 residues processed: 187 average time/residue: 0.1072 time to fit residues: 27.9408 Evaluate side-chains 159 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 509 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 796 ASN A1044 ASN B 501 GLN B 564 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.204069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.158944 restraints weight = 9894.654| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.82 r_work: 0.3594 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10016 Z= 0.160 Angle : 0.625 9.169 13529 Z= 0.315 Chirality : 0.043 0.186 1479 Planarity : 0.004 0.053 1735 Dihedral : 13.251 179.664 1358 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 1.13 % Allowed : 9.53 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1184 helix: 1.58 (0.22), residues: 568 sheet: -1.29 (0.42), residues: 145 loop : -0.92 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 808 TYR 0.024 0.001 TYR B 556 PHE 0.029 0.002 PHE B 355 TRP 0.016 0.001 TRP A 780 HIS 0.019 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00385 (10016) covalent geometry : angle 0.62465 (13529) hydrogen bonds : bond 0.04286 ( 492) hydrogen bonds : angle 4.44985 ( 1422) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.387 Fit side-chains REVERT: A 189 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7502 (mm-40) REVERT: A 232 MET cc_start: 0.4790 (OUTLIER) cc_final: 0.4257 (tpt) REVERT: A 493 GLU cc_start: 0.7550 (mp0) cc_final: 0.7159 (mp0) REVERT: A 822 ASN cc_start: 0.7992 (m-40) cc_final: 0.7411 (t0) REVERT: A 833 MET cc_start: 0.7360 (mtm) cc_final: 0.7111 (mtm) REVERT: A 858 MET cc_start: 0.7713 (tpp) cc_final: 0.7414 (tpp) outliers start: 12 outliers final: 6 residues processed: 166 average time/residue: 0.1168 time to fit residues: 26.7748 Evaluate side-chains 155 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN A 701 HIS A 703 ASN A 917 HIS A1042 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.203312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.159404 restraints weight = 9918.601| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.76 r_work: 0.3563 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10016 Z= 0.164 Angle : 0.575 8.148 13529 Z= 0.292 Chirality : 0.041 0.167 1479 Planarity : 0.004 0.032 1735 Dihedral : 12.340 175.256 1351 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.74 % Favored : 94.17 % Rotamer: Outliers : 2.36 % Allowed : 11.98 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1184 helix: 1.55 (0.22), residues: 566 sheet: -1.26 (0.41), residues: 158 loop : -0.90 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.021 0.001 TYR B 556 PHE 0.017 0.002 PHE A 937 TRP 0.022 0.002 TRP A 780 HIS 0.006 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00402 (10016) covalent geometry : angle 0.57465 (13529) hydrogen bonds : bond 0.03926 ( 492) hydrogen bonds : angle 4.21676 ( 1422) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.402 Fit side-chains REVERT: A 493 GLU cc_start: 0.7819 (mp0) cc_final: 0.7323 (mp0) REVERT: A 494 GLU cc_start: 0.7966 (tp30) cc_final: 0.7733 (tp30) REVERT: A 822 ASN cc_start: 0.7822 (m-40) cc_final: 0.7389 (t0) REVERT: A 833 MET cc_start: 0.7618 (mtm) cc_final: 0.7297 (mtt) REVERT: A 858 MET cc_start: 0.7526 (tpp) cc_final: 0.7235 (tpp) REVERT: A 977 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6905 (m-80) outliers start: 25 outliers final: 16 residues processed: 169 average time/residue: 0.1035 time to fit residues: 24.4355 Evaluate side-chains 158 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 578 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 0.0020 chunk 35 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 0.0050 chunk 7 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 180 HIS A 703 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.206319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.163769 restraints weight = 9873.652| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.78 r_work: 0.3574 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10016 Z= 0.115 Angle : 0.537 8.178 13529 Z= 0.271 Chirality : 0.040 0.160 1479 Planarity : 0.003 0.029 1735 Dihedral : 12.050 176.995 1348 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 2.36 % Allowed : 13.58 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 1184 helix: 1.78 (0.22), residues: 568 sheet: -1.22 (0.39), residues: 167 loop : -0.96 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 979 TYR 0.018 0.001 TYR B 556 PHE 0.014 0.001 PHE B 355 TRP 0.020 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00271 (10016) covalent geometry : angle 0.53668 (13529) hydrogen bonds : bond 0.03439 ( 492) hydrogen bonds : angle 4.03498 ( 1422) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.343 Fit side-chains REVERT: A 345 ASN cc_start: 0.6519 (t0) cc_final: 0.5345 (p0) REVERT: A 493 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: A 494 GLU cc_start: 0.8022 (tp30) cc_final: 0.7622 (tp30) REVERT: A 789 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6412 (mmm) REVERT: A 833 MET cc_start: 0.7453 (mtm) cc_final: 0.7173 (mtt) REVERT: A 858 MET cc_start: 0.7340 (tpp) cc_final: 0.6955 (tpp) REVERT: A 859 GLN cc_start: 0.7639 (mt0) cc_final: 0.7355 (mt0) REVERT: A 977 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6935 (m-80) outliers start: 25 outliers final: 12 residues processed: 170 average time/residue: 0.0955 time to fit residues: 22.8243 Evaluate side-chains 157 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 578 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 107 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 920 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 = 0.4321 r_free = 0.4321 target = 0.205648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.160472 restraints weight = 9847.898| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.81 r_work: 0.3574 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10016 Z= 0.124 Angle : 0.533 7.569 13529 Z= 0.269 Chirality : 0.040 0.168 1479 Planarity : 0.003 0.029 1735 Dihedral : 11.933 175.221 1348 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 2.17 % Allowed : 15.38 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1184 helix: 1.80 (0.22), residues: 568 sheet: -1.04 (0.41), residues: 158 loop : -0.90 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 562 TYR 0.017 0.001 TYR B 556 PHE 0.012 0.001 PHE A 667 TRP 0.017 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00297 (10016) covalent geometry : angle 0.53309 (13529) hydrogen bonds : bond 0.03380 ( 492) hydrogen bonds : angle 3.94843 ( 1422) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.259 Fit side-chains REVERT: A 345 ASN cc_start: 0.6563 (t0) cc_final: 0.5341 (p0) REVERT: A 474 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7707 (mm-30) REVERT: A 493 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.5938 (mt-10) REVERT: A 494 GLU cc_start: 0.7952 (tp30) cc_final: 0.7578 (tp30) REVERT: A 833 MET cc_start: 0.7448 (mtm) cc_final: 0.7221 (mtt) REVERT: A 858 MET cc_start: 0.7320 (tpp) cc_final: 0.6894 (tpp) REVERT: A 859 GLN cc_start: 0.7597 (mt0) cc_final: 0.7298 (mt0) REVERT: A 977 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6776 (m-80) REVERT: B 347 LEU cc_start: 0.5365 (OUTLIER) cc_final: 0.4760 (mt) REVERT: B 476 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6703 (tp30) outliers start: 23 outliers final: 13 residues processed: 161 average time/residue: 0.1089 time to fit residues: 24.2744 Evaluate side-chains 160 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 578 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 58 optimal weight: 0.1980 chunk 49 optimal weight: 0.0000 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 213 HIS ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.204593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161550 restraints weight = 9924.922| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.75 r_work: 0.3564 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10016 Z= 0.151 Angle : 0.547 7.397 13529 Z= 0.277 Chirality : 0.040 0.160 1479 Planarity : 0.003 0.031 1735 Dihedral : 11.972 176.349 1348 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.45 % Allowed : 16.23 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1184 helix: 1.72 (0.22), residues: 568 sheet: -1.17 (0.40), residues: 160 loop : -0.93 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.018 0.001 TYR B 556 PHE 0.013 0.002 PHE A 667 TRP 0.015 0.001 TRP A 780 HIS 0.010 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00372 (10016) covalent geometry : angle 0.54705 (13529) hydrogen bonds : bond 0.03504 ( 492) hydrogen bonds : angle 3.97028 ( 1422) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.390 Fit side-chains REVERT: A 345 ASN cc_start: 0.6604 (t0) cc_final: 0.5413 (p0) REVERT: A 474 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: A 493 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.5771 (mt-10) REVERT: A 494 GLU cc_start: 0.8013 (tp30) cc_final: 0.7662 (tp30) REVERT: A 499 SER cc_start: 0.6817 (t) cc_final: 0.6047 (m) REVERT: A 822 ASN cc_start: 0.7774 (m-40) cc_final: 0.7318 (t0) REVERT: A 858 MET cc_start: 0.7305 (tpp) cc_final: 0.6874 (tpp) REVERT: A 933 ASP cc_start: 0.6473 (p0) cc_final: 0.6259 (p0) REVERT: A 977 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6800 (m-80) REVERT: B 347 LEU cc_start: 0.5371 (OUTLIER) cc_final: 0.4760 (mt) REVERT: B 476 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6707 (tp30) REVERT: B 499 GLN cc_start: 0.6311 (tm-30) cc_final: 0.6022 (tm-30) outliers start: 26 outliers final: 17 residues processed: 172 average time/residue: 0.1034 time to fit residues: 24.9781 Evaluate side-chains 169 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 578 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 703 ASN A 728 GLN A 920 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.207029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.162540 restraints weight = 9817.723| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.70 r_work: 0.3598 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10016 Z= 0.111 Angle : 0.514 7.461 13529 Z= 0.260 Chirality : 0.039 0.159 1479 Planarity : 0.003 0.031 1735 Dihedral : 11.871 178.663 1348 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.45 % Allowed : 16.51 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1184 helix: 1.86 (0.22), residues: 569 sheet: -1.04 (0.41), residues: 158 loop : -0.87 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 562 TYR 0.016 0.001 TYR B 556 PHE 0.011 0.001 PHE A 667 TRP 0.015 0.001 TRP A 780 HIS 0.004 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00264 (10016) covalent geometry : angle 0.51411 (13529) hydrogen bonds : bond 0.03222 ( 492) hydrogen bonds : angle 3.84734 ( 1422) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.486 Fit side-chains REVERT: A 345 ASN cc_start: 0.6517 (t0) cc_final: 0.5359 (p0) REVERT: A 474 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: A 493 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: A 499 SER cc_start: 0.6761 (t) cc_final: 0.6062 (m) REVERT: A 675 MET cc_start: 0.7928 (ttp) cc_final: 0.7684 (ttp) REVERT: A 772 MET cc_start: 0.8039 (mmm) cc_final: 0.7380 (mmm) REVERT: A 822 ASN cc_start: 0.7760 (m-40) cc_final: 0.7296 (t0) REVERT: A 858 MET cc_start: 0.7177 (tpp) cc_final: 0.6810 (tpp) REVERT: A 977 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: B 347 LEU cc_start: 0.5348 (OUTLIER) cc_final: 0.4796 (mt) REVERT: B 476 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6598 (tp30) REVERT: B 501 GLN cc_start: 0.6052 (OUTLIER) cc_final: 0.5522 (tt0) outliers start: 26 outliers final: 16 residues processed: 164 average time/residue: 0.1171 time to fit residues: 26.3895 Evaluate side-chains 163 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 578 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 48 optimal weight: 0.0050 chunk 74 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.204825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.160017 restraints weight = 9852.583| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.74 r_work: 0.3561 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10016 Z= 0.157 Angle : 0.547 7.412 13529 Z= 0.278 Chirality : 0.040 0.158 1479 Planarity : 0.003 0.030 1735 Dihedral : 11.868 177.561 1348 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.74 % Allowed : 17.08 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1184 helix: 1.73 (0.22), residues: 569 sheet: -1.17 (0.41), residues: 158 loop : -0.88 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 373 TYR 0.017 0.001 TYR B 556 PHE 0.013 0.002 PHE A 667 TRP 0.013 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00385 (10016) covalent geometry : angle 0.54745 (13529) hydrogen bonds : bond 0.03479 ( 492) hydrogen bonds : angle 3.94795 ( 1422) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.392 Fit side-chains REVERT: A 345 ASN cc_start: 0.6574 (t0) cc_final: 0.5419 (p0) REVERT: A 474 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: A 493 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: A 499 SER cc_start: 0.6771 (t) cc_final: 0.6106 (m) REVERT: A 675 MET cc_start: 0.8035 (ttp) cc_final: 0.7772 (ttp) REVERT: A 772 MET cc_start: 0.8224 (mmm) cc_final: 0.7558 (mmm) REVERT: A 822 ASN cc_start: 0.7793 (m-40) cc_final: 0.7342 (t0) REVERT: A 858 MET cc_start: 0.7150 (tpp) cc_final: 0.6791 (tpp) REVERT: A 977 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.6698 (m-80) REVERT: B 347 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.4859 (mp) REVERT: B 476 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6665 (tp30) REVERT: B 499 GLN cc_start: 0.6278 (tm-30) cc_final: 0.5986 (tm-30) REVERT: B 501 GLN cc_start: 0.5973 (OUTLIER) cc_final: 0.5610 (tt0) outliers start: 29 outliers final: 19 residues processed: 170 average time/residue: 0.1018 time to fit residues: 24.3343 Evaluate side-chains 168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 578 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 703 ASN A 920 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.205163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.162451 restraints weight = 9844.905| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.72 r_work: 0.3583 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10016 Z= 0.146 Angle : 0.543 7.489 13529 Z= 0.276 Chirality : 0.040 0.159 1479 Planarity : 0.003 0.031 1735 Dihedral : 11.845 178.485 1348 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.83 % Allowed : 17.45 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1184 helix: 1.72 (0.22), residues: 569 sheet: -1.12 (0.41), residues: 156 loop : -0.86 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.017 0.001 TYR B 556 PHE 0.012 0.002 PHE A 667 TRP 0.014 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00357 (10016) covalent geometry : angle 0.54331 (13529) hydrogen bonds : bond 0.03437 ( 492) hydrogen bonds : angle 3.94639 ( 1422) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.267 Fit side-chains REVERT: A 330 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7459 (mt) REVERT: A 345 ASN cc_start: 0.6605 (t0) cc_final: 0.5362 (p0) REVERT: A 474 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7946 (mm-30) REVERT: A 493 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: A 499 SER cc_start: 0.6750 (t) cc_final: 0.6080 (m) REVERT: A 675 MET cc_start: 0.8014 (ttp) cc_final: 0.7766 (ttp) REVERT: A 772 MET cc_start: 0.8429 (mmm) cc_final: 0.7835 (mmm) REVERT: A 822 ASN cc_start: 0.7976 (m-40) cc_final: 0.7409 (t0) REVERT: A 858 MET cc_start: 0.7236 (tpp) cc_final: 0.6832 (tpp) REVERT: A 977 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.6902 (m-80) REVERT: B 347 LEU cc_start: 0.5443 (OUTLIER) cc_final: 0.4871 (mp) REVERT: B 476 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6829 (tp30) REVERT: B 501 GLN cc_start: 0.5977 (OUTLIER) cc_final: 0.5485 (tt0) outliers start: 30 outliers final: 19 residues processed: 169 average time/residue: 0.1009 time to fit residues: 23.5751 Evaluate side-chains 168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 578 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 703 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.203782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.158848 restraints weight = 9822.172| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.73 r_work: 0.3565 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10016 Z= 0.158 Angle : 0.560 7.469 13529 Z= 0.284 Chirality : 0.041 0.165 1479 Planarity : 0.003 0.033 1735 Dihedral : 11.817 178.320 1348 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.92 % Allowed : 17.26 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1184 helix: 1.68 (0.22), residues: 569 sheet: -1.23 (0.40), residues: 158 loop : -0.90 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.017 0.001 TYR B 556 PHE 0.013 0.002 PHE A 667 TRP 0.013 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00389 (10016) covalent geometry : angle 0.56040 (13529) hydrogen bonds : bond 0.03521 ( 492) hydrogen bonds : angle 3.98298 ( 1422) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.313 Fit side-chains REVERT: A 345 ASN cc_start: 0.6552 (t0) cc_final: 0.5395 (p0) REVERT: A 418 GLU cc_start: 0.7883 (pm20) cc_final: 0.7539 (pm20) REVERT: A 474 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7635 (mm-30) REVERT: A 493 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: A 499 SER cc_start: 0.6727 (t) cc_final: 0.6072 (m) REVERT: A 675 MET cc_start: 0.8010 (ttp) cc_final: 0.7736 (ttp) REVERT: A 772 MET cc_start: 0.8224 (mmm) cc_final: 0.7546 (mmm) REVERT: A 822 ASN cc_start: 0.7791 (m-40) cc_final: 0.7341 (t0) REVERT: A 858 MET cc_start: 0.7051 (tpp) cc_final: 0.6686 (tpp) REVERT: A 977 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6918 (m-80) REVERT: B 347 LEU cc_start: 0.5330 (OUTLIER) cc_final: 0.4783 (mp) REVERT: B 476 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7013 (tp30) REVERT: B 499 GLN cc_start: 0.6345 (tm-30) cc_final: 0.6085 (tm-30) REVERT: B 501 GLN cc_start: 0.6028 (OUTLIER) cc_final: 0.5528 (tt0) REVERT: B 555 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7177 (tm-30) REVERT: B 564 ASN cc_start: 0.7211 (t0) cc_final: 0.6823 (t0) outliers start: 31 outliers final: 21 residues processed: 169 average time/residue: 0.1046 time to fit residues: 24.4355 Evaluate side-chains 174 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 578 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 44 optimal weight: 0.3980 chunk 117 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 99 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 11 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN A 920 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.206741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.162946 restraints weight = 9810.598| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.77 r_work: 0.3593 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10016 Z= 0.113 Angle : 0.531 7.525 13529 Z= 0.269 Chirality : 0.039 0.174 1479 Planarity : 0.003 0.045 1735 Dihedral : 11.725 178.813 1348 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.36 % Allowed : 17.74 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.25), residues: 1184 helix: 1.86 (0.22), residues: 569 sheet: -1.06 (0.41), residues: 156 loop : -0.84 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 382 TYR 0.019 0.001 TYR A1038 PHE 0.012 0.001 PHE A 550 TRP 0.014 0.001 TRP A 780 HIS 0.004 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00271 (10016) covalent geometry : angle 0.53050 (13529) hydrogen bonds : bond 0.03198 ( 492) hydrogen bonds : angle 3.86140 ( 1422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2357.71 seconds wall clock time: 41 minutes 8.13 seconds (2468.13 seconds total)