Starting phenix.real_space_refine on Wed Mar 12 19:56:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rpj_24616/03_2025/7rpj_24616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rpj_24616/03_2025/7rpj_24616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rpj_24616/03_2025/7rpj_24616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rpj_24616/03_2025/7rpj_24616.map" model { file = "/net/cci-nas-00/data/ceres_data/7rpj_24616/03_2025/7rpj_24616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rpj_24616/03_2025/7rpj_24616.cif" } resolution = 3.2 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= -0.136 sd= 0.580 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 64 5.16 5 C 5277 2.51 5 N 1188 2.21 5 O 1397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7926 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7366 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 926, 7358 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 926, 7358 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885} Chain breaks: 3 bond proxies already assigned to first conformer: 7547 Chain: "A" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 560 Unusual residues: {'NAG': 5, 'Y01': 14} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALEU A1035 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A1035 " occ=0.50 Time building chain proxies: 8.44, per 1000 atoms: 1.06 Number of scatterers: 7926 At special positions: 0 Unit cell: (86.736, 87.57, 124.266, 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 64 16.00 O 1397 8.00 N 1188 7.00 C 5277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 366 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.02 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 829 " - pdb=" SG CYS A 849 " distance=2.02 Simple disulfide: pdb=" SG CYS A 863 " - pdb=" SG CYS A 872 " distance=2.02 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 887 " distance=2.03 Simple disulfide: pdb=" SG CYS A1127 " - pdb=" SG CYS A1131 " distance=2.10 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 Links applied NAG-ASN " NAG A1601 " - " ASN A 475 " " NAG A1602 " - " ASN A 834 " " NAG A1603 " - " ASN A 915 " " NAG A1604 " - " ASN A 390 " " NAG A1605 " - " ASN A 362 " Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.9 seconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 67.1% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 187 through 209 removed outlier: 3.777A pdb=" N VAL A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 243 Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.754A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.927A pdb=" N ALA A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 391 removed outlier: 5.264A pdb=" N LYS A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N HIS A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 4.065A pdb=" N LYS A 419 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.913A pdb=" N GLN A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 503 through 522 Processing helix chain 'A' and resid 524 through 547 removed outlier: 3.776A pdb=" N LEU A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 587 removed outlier: 4.125A pdb=" N THR A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 621 removed outlier: 5.076A pdb=" N LEU A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 626 through 662 removed outlier: 4.331A pdb=" N LEU A 651 " --> pdb=" O MET A 647 " (cutoff:3.500A) Proline residue: A 652 - end of helix Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 682 through 706 removed outlier: 4.109A pdb=" N CYS A 686 " --> pdb=" O TRP A 682 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLN A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 715 through 736 Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.847A pdb=" N TYR A 762 " --> pdb=" O PRO A 758 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 769 Processing helix chain 'A' and resid 770 through 777 Processing helix chain 'A' and resid 818 through 835 removed outlier: 3.594A pdb=" N GLN A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 861 removed outlier: 3.910A pdb=" N THR A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 895 removed outlier: 4.268A pdb=" N LYS A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 954 removed outlier: 3.635A pdb=" N SER A 954 " --> pdb=" O SER A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 963 removed outlier: 3.914A pdb=" N ARG A 962 " --> pdb=" O GLY A 959 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 963 " --> pdb=" O LEU A 960 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 959 through 963' Processing helix chain 'A' and resid 969 through 1002 removed outlier: 3.626A pdb=" N ASP A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1028 Processing helix chain 'A' and resid 1033 through 1061 removed outlier: 4.386A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1095 removed outlier: 5.364A pdb=" N SER A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ALA A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1123 Processing helix chain 'A' and resid 1123 through 1133 Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 4.452A pdb=" N GLY A1139 " --> pdb=" O GLY A1136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 451 through 458 removed outlier: 4.231A pdb=" N SER A 300 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA A 305 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL A 483 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 909 through 912 removed outlier: 3.521A pdb=" N ALA A 920 " --> pdb=" O ARG A 911 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N MET A 783 " --> pdb=" O SER A 927 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1308 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: 2.28 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1387 1.32 - 1.45: 2290 1.45 - 1.58: 4389 1.58 - 1.71: 5 1.71 - 1.84: 96 Bond restraints: 8167 Sorted by residual: bond pdb=" CA TYR A 245 " pdb=" C TYR A 245 " ideal model delta sigma weight residual 1.528 1.578 -0.051 8.80e-03 1.29e+04 3.32e+01 bond pdb=" N ARG A 225 " pdb=" CA ARG A 225 " ideal model delta sigma weight residual 1.457 1.407 0.050 1.24e-02 6.50e+03 1.63e+01 bond pdb=" C5 NAG A1605 " pdb=" O5 NAG A1605 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG A1604 " pdb=" O5 NAG A1604 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C5 NAG A1603 " pdb=" O5 NAG A1603 " ideal model delta sigma weight residual 1.413 1.484 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 8162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 9365 2.34 - 4.67: 1669 4.67 - 7.01: 139 7.01 - 9.34: 11 9.34 - 11.68: 3 Bond angle restraints: 11187 Sorted by residual: angle pdb=" N GLY A 394 " pdb=" CA GLY A 394 " pdb=" C GLY A 394 " ideal model delta sigma weight residual 112.00 120.19 -8.19 1.20e+00 6.94e-01 4.66e+01 angle pdb=" C TYR A 869 " pdb=" N PRO A 870 " pdb=" CA PRO A 870 " ideal model delta sigma weight residual 119.56 113.30 6.26 1.01e+00 9.80e-01 3.85e+01 angle pdb=" N ASP A 916 " pdb=" CA ASP A 916 " pdb=" C ASP A 916 " ideal model delta sigma weight residual 111.90 119.33 -7.43 1.32e+00 5.74e-01 3.16e+01 angle pdb=" N CYS A1127 " pdb=" CA CYS A1127 " pdb=" CB CYS A1127 " ideal model delta sigma weight residual 109.91 117.28 -7.37 1.46e+00 4.69e-01 2.55e+01 angle pdb=" CB HIS A 332 " pdb=" CG HIS A 332 " pdb=" CD2 HIS A 332 " ideal model delta sigma weight residual 131.20 124.70 6.50 1.30e+00 5.92e-01 2.50e+01 ... (remaining 11182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 4992 16.83 - 33.65: 419 33.65 - 50.48: 116 50.48 - 67.30: 24 67.30 - 84.13: 6 Dihedral angle restraints: 5557 sinusoidal: 2829 harmonic: 2728 Sorted by residual: dihedral pdb=" CB CYS A 384 " pdb=" SG CYS A 384 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 177.13 -84.13 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" C ASP A 916 " pdb=" N ASP A 916 " pdb=" CA ASP A 916 " pdb=" CB ASP A 916 " ideal model delta harmonic sigma weight residual -122.60 -138.31 15.71 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" CA SER A 477 " pdb=" C SER A 477 " pdb=" N ASP A 478 " pdb=" CA ASP A 478 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 5554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 1236 0.193 - 0.385: 66 0.385 - 0.578: 2 0.578 - 0.770: 1 0.770 - 0.963: 1 Chirality restraints: 1306 Sorted by residual: chirality pdb=" C1 NAG A1604 " pdb=" ND2 ASN A 390 " pdb=" C2 NAG A1604 " pdb=" O5 NAG A1604 " both_signs ideal model delta sigma weight residual False -2.40 -3.36 0.96 2.00e-01 2.50e+01 2.32e+01 chirality pdb=" CA ASP A 916 " pdb=" N ASP A 916 " pdb=" C ASP A 916 " pdb=" CB ASP A 916 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA LYS A 522 " pdb=" N LYS A 522 " pdb=" C LYS A 522 " pdb=" CB LYS A 522 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 ... (remaining 1303 not shown) Planarity restraints: 1321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 362 " -0.136 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" CG ASN A 362 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN A 362 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 362 " 0.223 2.00e-02 2.50e+03 pdb=" C1 NAG A1605 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1030 " 0.133 2.00e-02 2.50e+03 7.56e-02 1.43e+02 pdb=" CG TRP A1030 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A1030 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A1030 " -0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP A1030 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 TRP A1030 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A1030 " -0.108 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1030 " 0.094 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1030 " -0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP A1030 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 283 " 0.124 2.00e-02 2.50e+03 6.86e-02 1.18e+02 pdb=" CG TRP A 283 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 283 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 283 " -0.098 2.00e-02 2.50e+03 pdb=" NE1 TRP A 283 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP A 283 " -0.031 2.00e-02 2.50e+03 pdb=" CE3 TRP A 283 " -0.092 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 283 " 0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 283 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 283 " 0.085 2.00e-02 2.50e+03 ... (remaining 1318 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 3763 2.95 - 3.43: 8917 3.43 - 3.92: 13016 3.92 - 4.41: 15341 4.41 - 4.90: 24375 Nonbonded interactions: 65412 Sorted by model distance: nonbonded pdb=" OD1 ASP A 896 " pdb=" NE2 HIS A 902 " model vdw 2.458 3.120 nonbonded pdb=" O THR A 392 " pdb=" N CYS A 410 " model vdw 2.557 3.120 nonbonded pdb=" OD1 ASP A 845 " pdb=" OG1 THR A 847 " model vdw 2.559 3.040 nonbonded pdb=" O VAL A1113 " pdb=" OG SER A1117 " model vdw 2.560 3.040 nonbonded pdb=" O PHE A 694 " pdb=" OG SER A 697 " model vdw 2.564 3.040 ... (remaining 65407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.110 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 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 : 0.014 0.078 8167 Z= 0.868 Angle : 1.718 11.678 11187 Z= 1.114 Chirality : 0.105 0.963 1306 Planarity : 0.014 0.130 1316 Dihedral : 13.324 77.694 3764 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.42 % Rotamer: Outliers : 0.98 % Allowed : 5.41 % Favored : 93.61 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.26), residues: 921 helix: -0.99 (0.19), residues: 557 sheet: -0.48 (0.95), residues: 29 loop : -1.06 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.133 0.025 TRP A1030 HIS 0.010 0.004 HIS A 782 PHE 0.100 0.014 PHE A 850 TYR 0.112 0.018 TYR A 942 ARG 0.011 0.001 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7291 (ttp) cc_final: 0.7047 (ttt) REVERT: A 211 GLU cc_start: 0.8630 (pm20) cc_final: 0.7854 (tp30) REVERT: A 369 ILE cc_start: 0.8712 (pt) cc_final: 0.8477 (mt) REVERT: A 448 LEU cc_start: 0.8654 (tp) cc_final: 0.8421 (tp) REVERT: A 449 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8485 (ttpp) REVERT: A 529 MET cc_start: 0.7455 (mmt) cc_final: 0.6703 (mmm) REVERT: A 647 MET cc_start: 0.7925 (mmt) cc_final: 0.7620 (mmm) REVERT: A 776 HIS cc_start: 0.8141 (t-90) cc_final: 0.7834 (t70) REVERT: A 794 GLU cc_start: 0.8533 (tt0) cc_final: 0.7836 (mp0) REVERT: A 869 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: A 940 GLN cc_start: 0.8865 (tt0) cc_final: 0.8651 (tp-100) REVERT: A 965 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7881 (t80) REVERT: A 1047 SER cc_start: 0.8335 (t) cc_final: 0.7918 (m) REVERT: A 1111 MET cc_start: 0.6999 (mtm) cc_final: 0.6652 (mtm) REVERT: A 1128 LEU cc_start: 0.8676 (mp) cc_final: 0.8458 (mp) outliers start: 7 outliers final: 2 residues processed: 137 average time/residue: 0.1995 time to fit residues: 37.6187 Evaluate side-chains 80 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 965 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.119069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.089044 restraints weight = 30718.872| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.87 r_work: 0.3213 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 8167 Z= 0.217 Angle : 0.735 17.755 11187 Z= 0.363 Chirality : 0.044 0.245 1306 Planarity : 0.004 0.043 1316 Dihedral : 9.767 59.028 2102 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.72 % Allowed : 11.06 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.61 (0.28), residues: 921 helix: 0.92 (0.21), residues: 571 sheet: 0.18 (0.96), residues: 29 loop : -0.38 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 789 HIS 0.005 0.001 HIS A 827 PHE 0.015 0.001 PHE A 618 TYR 0.021 0.002 TYR A1009 ARG 0.006 0.001 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7917 (ttp) cc_final: 0.7593 (ttp) REVERT: A 211 GLU cc_start: 0.8526 (pm20) cc_final: 0.7989 (tp30) REVERT: A 436 MET cc_start: 0.7299 (mmm) cc_final: 0.7006 (mmt) REVERT: A 524 MET cc_start: 0.7406 (ptp) cc_final: 0.6833 (ptt) REVERT: A 529 MET cc_start: 0.8821 (mmt) cc_final: 0.7815 (mmm) REVERT: A 582 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.6078 (t80) REVERT: A 693 LEU cc_start: 0.9276 (mp) cc_final: 0.8775 (pp) REVERT: A 869 TYR cc_start: 0.8852 (p90) cc_final: 0.8573 (m-10) REVERT: A 1047 SER cc_start: 0.9343 (t) cc_final: 0.8946 (m) REVERT: A 1132 LEU cc_start: 0.8061 (mt) cc_final: 0.7834 (mt) outliers start: 13 outliers final: 6 residues processed: 119 average time/residue: 0.1580 time to fit residues: 27.8562 Evaluate side-chains 83 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1127 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 GLN A 776 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.118712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.087278 restraints weight = 45938.849| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.79 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 8167 Z= 0.203 Angle : 0.671 12.928 11187 Z= 0.327 Chirality : 0.042 0.226 1306 Planarity : 0.004 0.043 1316 Dihedral : 9.340 59.818 2096 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.97 % Allowed : 13.39 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.28), residues: 921 helix: 1.30 (0.22), residues: 573 sheet: 0.51 (1.04), residues: 27 loop : -0.31 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 948 HIS 0.003 0.001 HIS A1053 PHE 0.015 0.001 PHE A 618 TYR 0.015 0.002 TYR A 869 ARG 0.004 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8236 (pm20) cc_final: 0.7908 (tp30) REVERT: A 348 CYS cc_start: 0.7736 (t) cc_final: 0.7256 (p) REVERT: A 512 ILE cc_start: 0.8642 (mm) cc_final: 0.8423 (mm) REVERT: A 524 MET cc_start: 0.6880 (ptp) cc_final: 0.6588 (ptt) REVERT: A 582 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.6158 (t80) REVERT: A 693 LEU cc_start: 0.9300 (mp) cc_final: 0.8823 (pp) REVERT: A 1047 SER cc_start: 0.9013 (t) cc_final: 0.8653 (m) REVERT: A 1094 MET cc_start: 0.8888 (tpp) cc_final: 0.8686 (tpp) REVERT: A 1095 MET cc_start: 0.8424 (mmm) cc_final: 0.8063 (mmp) outliers start: 15 outliers final: 7 residues processed: 93 average time/residue: 0.1482 time to fit residues: 21.2094 Evaluate side-chains 82 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1131 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 14 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.119550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.088884 restraints weight = 36160.400| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 4.28 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 8167 Z= 0.193 Angle : 0.642 11.945 11187 Z= 0.313 Chirality : 0.041 0.229 1306 Planarity : 0.004 0.043 1316 Dihedral : 9.242 59.731 2096 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.09 % Allowed : 14.13 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.28), residues: 921 helix: 1.44 (0.22), residues: 567 sheet: 0.65 (1.07), residues: 26 loop : -0.29 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 313 HIS 0.010 0.001 HIS A 777 PHE 0.025 0.001 PHE A 435 TYR 0.033 0.002 TYR A 388 ARG 0.003 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.7470 (mt) cc_final: 0.7093 (tp) REVERT: A 211 GLU cc_start: 0.8152 (pm20) cc_final: 0.7616 (tp30) REVERT: A 212 LEU cc_start: 0.8735 (mt) cc_final: 0.7695 (mp) REVERT: A 348 CYS cc_start: 0.7562 (t) cc_final: 0.7280 (p) REVERT: A 524 MET cc_start: 0.6774 (ptp) cc_final: 0.6475 (ptt) REVERT: A 582 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.6058 (t80) REVERT: A 693 LEU cc_start: 0.9324 (mp) cc_final: 0.8849 (pp) REVERT: A 998 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8173 (mm) outliers start: 16 outliers final: 11 residues processed: 97 average time/residue: 0.1442 time to fit residues: 21.7125 Evaluate side-chains 87 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1131 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 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 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.119097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.088998 restraints weight = 32213.894| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 4.01 r_work: 0.3213 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 8167 Z= 0.200 Angle : 0.627 12.673 11187 Z= 0.304 Chirality : 0.041 0.235 1306 Planarity : 0.004 0.044 1316 Dihedral : 9.129 59.509 2096 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.21 % Allowed : 13.51 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.28), residues: 921 helix: 1.56 (0.22), residues: 567 sheet: 0.67 (1.09), residues: 26 loop : -0.19 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 313 HIS 0.003 0.001 HIS A1053 PHE 0.022 0.001 PHE A 770 TYR 0.030 0.001 TYR A 388 ARG 0.004 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.7469 (mt) cc_final: 0.7064 (tp) REVERT: A 211 GLU cc_start: 0.8453 (pm20) cc_final: 0.7868 (tp30) REVERT: A 212 LEU cc_start: 0.8813 (mt) cc_final: 0.7832 (mp) REVERT: A 348 CYS cc_start: 0.7950 (t) cc_final: 0.7277 (p) REVERT: A 529 MET cc_start: 0.8837 (mmt) cc_final: 0.7871 (mmm) REVERT: A 582 TYR cc_start: 0.6445 (OUTLIER) cc_final: 0.5830 (t80) REVERT: A 693 LEU cc_start: 0.9298 (mp) cc_final: 0.8804 (pp) REVERT: A 998 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8347 (mm) outliers start: 17 outliers final: 11 residues processed: 95 average time/residue: 0.1834 time to fit residues: 27.5703 Evaluate side-chains 91 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1131 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.1980 chunk 11 optimal weight: 0.0170 chunk 65 optimal weight: 9.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.119942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.089438 restraints weight = 34193.915| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.17 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8167 Z= 0.174 Angle : 0.615 10.859 11187 Z= 0.296 Chirality : 0.040 0.239 1306 Planarity : 0.004 0.043 1316 Dihedral : 8.912 59.667 2096 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.21 % Allowed : 13.76 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.28), residues: 921 helix: 1.65 (0.22), residues: 568 sheet: 0.42 (1.08), residues: 26 loop : -0.23 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 948 HIS 0.003 0.001 HIS A1053 PHE 0.015 0.001 PHE A 435 TYR 0.025 0.001 TYR A 388 ARG 0.003 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.7387 (mt) cc_final: 0.7008 (tp) REVERT: A 211 GLU cc_start: 0.8109 (pm20) cc_final: 0.7717 (tp30) REVERT: A 212 LEU cc_start: 0.8745 (mt) cc_final: 0.7715 (mp) REVERT: A 452 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8626 (mmm) REVERT: A 529 MET cc_start: 0.8534 (mmt) cc_final: 0.7588 (mmm) REVERT: A 582 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.5980 (t80) REVERT: A 693 LEU cc_start: 0.9328 (mp) cc_final: 0.8852 (pp) REVERT: A 846 PHE cc_start: 0.7822 (m-10) cc_final: 0.6846 (p90) REVERT: A 1083 MET cc_start: 0.8483 (tpp) cc_final: 0.8185 (tpp) outliers start: 17 outliers final: 12 residues processed: 99 average time/residue: 0.1386 time to fit residues: 21.4389 Evaluate side-chains 92 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1132 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.120747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.090743 restraints weight = 35759.855| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.23 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 8167 Z= 0.178 Angle : 0.607 14.289 11187 Z= 0.295 Chirality : 0.039 0.244 1306 Planarity : 0.004 0.046 1316 Dihedral : 8.689 59.681 2096 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.33 % Allowed : 14.25 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.28), residues: 921 helix: 1.70 (0.22), residues: 565 sheet: 0.46 (1.12), residues: 26 loop : -0.19 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 650 HIS 0.002 0.001 HIS A 776 PHE 0.013 0.001 PHE A1019 TYR 0.021 0.001 TYR A 388 ARG 0.003 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.7380 (mt) cc_final: 0.7015 (tp) REVERT: A 211 GLU cc_start: 0.8095 (pm20) cc_final: 0.7716 (tp30) REVERT: A 212 LEU cc_start: 0.8758 (mt) cc_final: 0.7777 (mp) REVERT: A 452 MET cc_start: 0.8791 (tpp) cc_final: 0.8558 (mmm) REVERT: A 529 MET cc_start: 0.8521 (mmt) cc_final: 0.7637 (mmm) REVERT: A 582 TYR cc_start: 0.6462 (OUTLIER) cc_final: 0.5992 (t80) REVERT: A 693 LEU cc_start: 0.9320 (mp) cc_final: 0.8856 (pp) REVERT: A 771 MET cc_start: 0.7539 (mmm) cc_final: 0.7328 (mmm) REVERT: A 846 PHE cc_start: 0.7876 (m-10) cc_final: 0.6904 (p90) REVERT: A 986 MET cc_start: 0.8066 (mmm) cc_final: 0.7715 (tmm) REVERT: A 998 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8214 (mm) REVERT: A 1083 MET cc_start: 0.8444 (tpp) cc_final: 0.8169 (tpp) outliers start: 18 outliers final: 10 residues processed: 98 average time/residue: 0.1504 time to fit residues: 23.1445 Evaluate side-chains 90 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 HIS A 777 HIS A 874 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.117999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.087568 restraints weight = 31635.643| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.95 r_work: 0.3194 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 8167 Z= 0.253 Angle : 0.654 15.522 11187 Z= 0.317 Chirality : 0.041 0.237 1306 Planarity : 0.004 0.044 1316 Dihedral : 8.878 58.789 2096 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.33 % Allowed : 14.62 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.28), residues: 921 helix: 1.63 (0.22), residues: 567 sheet: 0.40 (1.16), residues: 26 loop : -0.22 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 650 HIS 0.006 0.001 HIS A 874 PHE 0.018 0.002 PHE A 750 TYR 0.022 0.002 TYR A 388 ARG 0.002 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.7497 (mt) cc_final: 0.7103 (tp) REVERT: A 211 GLU cc_start: 0.8465 (pm20) cc_final: 0.7919 (tp30) REVERT: A 212 LEU cc_start: 0.8830 (mt) cc_final: 0.7907 (mp) REVERT: A 452 MET cc_start: 0.9000 (tpp) cc_final: 0.8797 (mmm) REVERT: A 529 MET cc_start: 0.8750 (mmt) cc_final: 0.7931 (mmm) REVERT: A 582 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.5862 (t80) REVERT: A 693 LEU cc_start: 0.9310 (mp) cc_final: 0.8827 (pp) REVERT: A 771 MET cc_start: 0.8067 (mmm) cc_final: 0.7801 (mmm) REVERT: A 846 PHE cc_start: 0.8012 (m-10) cc_final: 0.6885 (p90) REVERT: A 998 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8383 (mm) outliers start: 18 outliers final: 14 residues processed: 93 average time/residue: 0.1356 time to fit residues: 19.9056 Evaluate side-chains 94 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 874 HIS Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.119245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088200 restraints weight = 44004.744| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 4.71 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 8167 Z= 0.194 Angle : 0.621 16.491 11187 Z= 0.303 Chirality : 0.040 0.241 1306 Planarity : 0.004 0.043 1316 Dihedral : 8.783 58.915 2096 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.09 % Allowed : 14.25 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 921 helix: 1.67 (0.22), residues: 567 sheet: 0.51 (1.18), residues: 26 loop : -0.23 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 650 HIS 0.004 0.001 HIS A 874 PHE 0.013 0.001 PHE A 435 TYR 0.020 0.001 TYR A 388 ARG 0.003 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.7386 (mt) cc_final: 0.7037 (tp) REVERT: A 211 GLU cc_start: 0.8147 (pm20) cc_final: 0.7750 (tp30) REVERT: A 212 LEU cc_start: 0.8779 (mt) cc_final: 0.7834 (mp) REVERT: A 452 MET cc_start: 0.8840 (tpp) cc_final: 0.8630 (mmm) REVERT: A 529 MET cc_start: 0.8479 (mmt) cc_final: 0.7607 (mmm) REVERT: A 582 TYR cc_start: 0.6355 (OUTLIER) cc_final: 0.5969 (t80) REVERT: A 693 LEU cc_start: 0.9328 (mp) cc_final: 0.8870 (pp) REVERT: A 771 MET cc_start: 0.7672 (mmm) cc_final: 0.7431 (mmm) REVERT: A 846 PHE cc_start: 0.7858 (m-10) cc_final: 0.6805 (p90) REVERT: A 998 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8194 (mm) outliers start: 16 outliers final: 12 residues processed: 95 average time/residue: 0.1386 time to fit residues: 20.6957 Evaluate side-chains 94 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.118642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.087520 restraints weight = 40505.984| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 4.51 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 8167 Z= 0.232 Angle : 0.634 16.814 11187 Z= 0.310 Chirality : 0.040 0.242 1306 Planarity : 0.004 0.043 1316 Dihedral : 8.812 58.479 2096 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.97 % Allowed : 14.37 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.28), residues: 921 helix: 1.61 (0.22), residues: 567 sheet: 0.53 (1.18), residues: 26 loop : -0.29 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 650 HIS 0.005 0.001 HIS A 874 PHE 0.015 0.001 PHE A 750 TYR 0.020 0.001 TYR A 388 ARG 0.002 0.000 ARG A 774 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.7419 (mt) cc_final: 0.7059 (tp) REVERT: A 211 GLU cc_start: 0.8110 (pm20) cc_final: 0.7759 (tp30) REVERT: A 212 LEU cc_start: 0.8775 (mt) cc_final: 0.7781 (mp) REVERT: A 529 MET cc_start: 0.8485 (mmt) cc_final: 0.7621 (mmm) REVERT: A 582 TYR cc_start: 0.6323 (OUTLIER) cc_final: 0.5986 (t80) REVERT: A 693 LEU cc_start: 0.9328 (mp) cc_final: 0.8868 (pp) REVERT: A 771 MET cc_start: 0.7698 (mmm) cc_final: 0.7469 (mmm) REVERT: A 846 PHE cc_start: 0.7794 (m-10) cc_final: 0.6748 (p90) REVERT: A 998 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8214 (mm) REVERT: A 1095 MET cc_start: 0.8171 (mmp) cc_final: 0.7933 (mmp) outliers start: 15 outliers final: 13 residues processed: 93 average time/residue: 0.1356 time to fit residues: 19.8625 Evaluate side-chains 96 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.119748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088824 restraints weight = 38456.204| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.43 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 8167 Z= 0.190 Angle : 0.611 17.001 11187 Z= 0.299 Chirality : 0.040 0.242 1306 Planarity : 0.004 0.043 1316 Dihedral : 8.657 58.423 2096 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.33 % Allowed : 14.13 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.28), residues: 921 helix: 1.64 (0.22), residues: 567 sheet: 0.58 (1.17), residues: 26 loop : -0.26 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 650 HIS 0.003 0.001 HIS A 776 PHE 0.013 0.001 PHE A 770 TYR 0.019 0.001 TYR A 388 ARG 0.002 0.000 ARG A 774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4193.57 seconds wall clock time: 73 minutes 28.71 seconds (4408.71 seconds total)