Starting phenix.real_space_refine on Tue Mar 3 19:14:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rpj_24616/03_2026/7rpj_24616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rpj_24616/03_2026/7rpj_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rpj_24616/03_2026/7rpj_24616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rpj_24616/03_2026/7rpj_24616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rpj_24616/03_2026/7rpj_24616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rpj_24616/03_2026/7rpj_24616.map" } resolution = 3.2 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= -0.136 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.15, per 1000 atoms: 0.40 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: 0.68 Conformation dependent library (CDL) restraints added in 455.8 milliseconds 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: 0.28 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: 1.04 Time building geometry restraints manager: 0.90 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.510 Find NCS groups from input model: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.580 ------------------------------------------------------------------------------- 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 0.280 8181 Z= 0.816 Angle : 1.746 22.488 11220 Z= 1.119 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 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: -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 ARG 0.011 0.001 ARG A 546 TYR 0.112 0.018 TYR A 942 PHE 0.100 0.014 PHE A 850 TRP 0.133 0.025 TRP A1030 HIS 0.010 0.004 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.01363 ( 8167) covalent geometry : angle 1.71755 (11187) SS BOND : bond 0.02282 ( 9) SS BOND : angle 3.77948 ( 18) hydrogen bonds : bond 0.16034 ( 447) hydrogen bonds : angle 8.14138 ( 1308) link_NAG-ASN : bond 0.12523 ( 5) link_NAG-ASN : angle 7.99718 ( 15) *********************** 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 : 0.287 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: 0.8320 (tp) REVERT: A 449 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8496 (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: 0.7619 (mmm) REVERT: A 776 HIS cc_start: 0.8141 (t-90) cc_final: 0.7835 (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: 0.8650 (tp-100) REVERT: A 965 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7880 (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: 0.0801 time to fit residues: 15.1666 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 : 0.196 ------------------------------------------------------------------------------- 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 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 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 387 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.119320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.088308 restraints weight = 42034.236| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 4.59 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 8181 Z= 0.147 Angle : 0.750 17.344 11220 Z= 0.365 Chirality : 0.044 0.258 1306 Planarity : 0.004 0.043 1316 Dihedral : 9.770 58.727 2102 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.72 % Allowed : 11.30 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.67 (0.28), residues: 921 helix: 0.96 (0.21), residues: 571 sheet: 0.30 (0.98), residues: 29 loop : -0.34 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 262 TYR 0.022 0.002 TYR A1009 PHE 0.016 0.001 PHE A 618 TRP 0.023 0.002 TRP A 948 HIS 0.005 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8167) covalent geometry : angle 0.73500 (11187) SS BOND : bond 0.01309 ( 9) SS BOND : angle 2.33996 ( 18) hydrogen bonds : bond 0.04725 ( 447) hydrogen bonds : angle 4.91698 ( 1308) link_NAG-ASN : bond 0.00385 ( 5) link_NAG-ASN : angle 3.35329 ( 15) *********************** 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 124 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8263 (pm20) cc_final: 0.7859 (tp30) REVERT: A 217 ASP cc_start: 0.8500 (t70) cc_final: 0.8273 (t70) REVERT: A 436 MET cc_start: 0.7036 (mmm) cc_final: 0.6801 (mmt) REVERT: A 524 MET cc_start: 0.7236 (ptp) cc_final: 0.6717 (ptt) REVERT: A 529 MET cc_start: 0.8575 (mmt) cc_final: 0.7575 (mmm) REVERT: A 582 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.6168 (t80) REVERT: A 693 LEU cc_start: 0.9297 (mp) cc_final: 0.8806 (pp) REVERT: A 1047 SER cc_start: 0.9089 (t) cc_final: 0.8687 (m) REVERT: A 1132 LEU cc_start: 0.7997 (mt) cc_final: 0.7794 (mt) outliers start: 13 outliers final: 5 residues processed: 122 average time/residue: 0.0684 time to fit residues: 12.3161 Evaluate side-chains 81 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 0.0060 chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.119811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.089317 restraints weight = 38327.807| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.37 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 8181 Z= 0.131 Angle : 0.667 12.430 11220 Z= 0.323 Chirality : 0.041 0.231 1306 Planarity : 0.004 0.046 1316 Dihedral : 9.224 59.813 2096 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.21 % Allowed : 13.64 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.16 (0.28), residues: 921 helix: 1.41 (0.22), residues: 574 sheet: 0.51 (1.04), residues: 27 loop : -0.28 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.026 0.002 TYR A 388 PHE 0.016 0.001 PHE A 618 TRP 0.022 0.002 TRP A 948 HIS 0.006 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8167) covalent geometry : angle 0.65267 (11187) SS BOND : bond 0.01077 ( 9) SS BOND : angle 2.30620 ( 18) hydrogen bonds : bond 0.04105 ( 447) hydrogen bonds : angle 4.55801 ( 1308) link_NAG-ASN : bond 0.00416 ( 5) link_NAG-ASN : angle 2.87178 ( 15) *********************** 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 110 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 198 LEU cc_start: 0.7418 (mt) cc_final: 0.7059 (tp) REVERT: A 211 GLU cc_start: 0.8178 (pm20) cc_final: 0.7880 (tp30) REVERT: A 212 LEU cc_start: 0.8707 (mt) cc_final: 0.8478 (mp) REVERT: A 217 ASP cc_start: 0.8357 (t70) cc_final: 0.8103 (t70) REVERT: A 348 CYS cc_start: 0.7598 (t) cc_final: 0.7184 (p) REVERT: A 582 TYR cc_start: 0.6596 (OUTLIER) cc_final: 0.5983 (t80) REVERT: A 693 LEU cc_start: 0.9317 (mp) cc_final: 0.8826 (pp) REVERT: A 869 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8625 (m-80) REVERT: A 983 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 1132 LEU cc_start: 0.7582 (mt) cc_final: 0.7252 (tp) outliers start: 17 outliers final: 7 residues processed: 103 average time/residue: 0.0609 time to fit residues: 9.7910 Evaluate side-chains 90 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 582 TYR 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 983 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.118857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.087415 restraints weight = 49850.273| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 5.02 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 8181 Z= 0.146 Angle : 0.663 12.196 11220 Z= 0.319 Chirality : 0.041 0.229 1306 Planarity : 0.004 0.047 1316 Dihedral : 9.282 59.973 2096 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.97 % Allowed : 14.25 % 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 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: 1.24 (0.28), residues: 921 helix: 1.48 (0.22), residues: 569 sheet: 0.46 (1.05), residues: 27 loop : -0.24 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.027 0.002 TYR A 388 PHE 0.024 0.001 PHE A 435 TRP 0.022 0.002 TRP A 313 HIS 0.003 0.001 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8167) covalent geometry : angle 0.64950 (11187) SS BOND : bond 0.01103 ( 9) SS BOND : angle 2.26958 ( 18) hydrogen bonds : bond 0.04055 ( 447) hydrogen bonds : angle 4.54721 ( 1308) link_NAG-ASN : bond 0.00424 ( 5) link_NAG-ASN : angle 2.74446 ( 15) *********************** 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 99 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.7478 (mt) cc_final: 0.7103 (tp) REVERT: A 211 GLU cc_start: 0.8165 (pm20) cc_final: 0.7616 (tp30) REVERT: A 212 LEU cc_start: 0.8756 (mt) cc_final: 0.7728 (mp) REVERT: A 217 ASP cc_start: 0.8377 (t70) cc_final: 0.8105 (t70) REVERT: A 348 CYS cc_start: 0.7758 (t) cc_final: 0.7399 (p) REVERT: A 529 MET cc_start: 0.8544 (mmt) cc_final: 0.7654 (mmm) REVERT: A 531 MET cc_start: 0.8502 (tpp) cc_final: 0.8212 (mmp) REVERT: A 582 TYR cc_start: 0.6594 (OUTLIER) cc_final: 0.6026 (t80) REVERT: A 693 LEU cc_start: 0.9327 (mp) cc_final: 0.8839 (pp) REVERT: A 983 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8470 (tt) REVERT: A 1132 LEU cc_start: 0.7497 (mt) cc_final: 0.7241 (tp) outliers start: 15 outliers final: 11 residues processed: 94 average time/residue: 0.0575 time to fit residues: 8.6582 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 : 0.271 ------------------------------------------------------------------------------- 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 696 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 983 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 44 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 67 optimal weight: 0.0970 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.120452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.090912 restraints weight = 35972.675| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 4.20 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 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 = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 8181 Z= 0.120 Angle : 0.631 11.538 11220 Z= 0.302 Chirality : 0.040 0.238 1306 Planarity : 0.004 0.048 1316 Dihedral : 8.990 59.558 2096 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.97 % Allowed : 14.50 % 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 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: 1.41 (0.28), residues: 921 helix: 1.60 (0.22), residues: 568 sheet: 0.52 (1.08), residues: 26 loop : -0.14 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.023 0.001 TYR A 388 PHE 0.017 0.001 PHE A 435 TRP 0.018 0.001 TRP A 948 HIS 0.003 0.001 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8167) covalent geometry : angle 0.61618 (11187) SS BOND : bond 0.00775 ( 9) SS BOND : angle 2.47680 ( 18) hydrogen bonds : bond 0.03696 ( 447) hydrogen bonds : angle 4.40456 ( 1308) link_NAG-ASN : bond 0.00500 ( 5) link_NAG-ASN : angle 2.62516 ( 15) *********************** 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 106 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.7423 (mt) cc_final: 0.7051 (tp) REVERT: A 211 GLU cc_start: 0.8050 (pm20) cc_final: 0.7701 (tp30) REVERT: A 212 LEU cc_start: 0.8698 (mt) cc_final: 0.7678 (mp) REVERT: A 217 ASP cc_start: 0.8217 (t70) cc_final: 0.7945 (t70) REVERT: A 529 MET cc_start: 0.8498 (mmt) cc_final: 0.7602 (mmm) REVERT: A 582 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5927 (t80) REVERT: A 693 LEU cc_start: 0.9322 (mp) cc_final: 0.8853 (pp) REVERT: A 846 PHE cc_start: 0.7782 (m-10) cc_final: 0.6810 (p90) REVERT: A 983 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8440 (tt) REVERT: A 998 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8158 (mm) REVERT: A 1083 MET cc_start: 0.8459 (tpp) cc_final: 0.8173 (tpp) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.0632 time to fit residues: 9.8453 Evaluate side-chains 91 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 983 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.0670 chunk 58 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 chunk 74 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.121619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090308 restraints weight = 49977.900| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 5.12 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8181 Z= 0.116 Angle : 0.630 13.594 11220 Z= 0.299 Chirality : 0.039 0.239 1306 Planarity : 0.004 0.047 1316 Dihedral : 8.762 59.457 2094 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.97 % Allowed : 13.88 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.48 (0.28), residues: 921 helix: 1.71 (0.22), residues: 568 sheet: 0.42 (1.06), residues: 26 loop : -0.18 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.021 0.001 TYR A 388 PHE 0.015 0.001 PHE A 435 TRP 0.017 0.001 TRP A 948 HIS 0.002 0.000 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8167) covalent geometry : angle 0.61579 (11187) SS BOND : bond 0.01014 ( 9) SS BOND : angle 2.54965 ( 18) hydrogen bonds : bond 0.03570 ( 447) hydrogen bonds : angle 4.31588 ( 1308) link_NAG-ASN : bond 0.00517 ( 5) link_NAG-ASN : angle 2.58286 ( 15) *********************** 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 106 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8140 (pm20) cc_final: 0.7679 (tp30) REVERT: A 212 LEU cc_start: 0.8733 (mt) cc_final: 0.7838 (mp) REVERT: A 531 MET cc_start: 0.8448 (tpp) cc_final: 0.8207 (mmp) REVERT: A 582 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.5994 (t80) REVERT: A 693 LEU cc_start: 0.9325 (mp) cc_final: 0.8866 (pp) REVERT: A 771 MET cc_start: 0.7617 (mmm) cc_final: 0.7376 (mmm) REVERT: A 846 PHE cc_start: 0.7832 (m-10) cc_final: 0.6829 (p90) REVERT: A 998 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8153 (mm) REVERT: A 1083 MET cc_start: 0.8454 (tpp) cc_final: 0.8190 (tpp) outliers start: 15 outliers final: 7 residues processed: 101 average time/residue: 0.0604 time to fit residues: 9.5903 Evaluate side-chains 88 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.118870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.088675 restraints weight = 31600.524| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.93 r_work: 0.3220 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 8181 Z= 0.153 Angle : 0.660 14.936 11220 Z= 0.316 Chirality : 0.041 0.239 1306 Planarity : 0.004 0.044 1316 Dihedral : 8.827 59.433 2094 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.97 % Allowed : 14.13 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.44 (0.28), residues: 921 helix: 1.67 (0.22), residues: 569 sheet: 0.47 (1.07), residues: 26 loop : -0.19 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.019 0.001 TYR A 388 PHE 0.016 0.001 PHE A 750 TRP 0.036 0.002 TRP A 650 HIS 0.002 0.001 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8167) covalent geometry : angle 0.64522 (11187) SS BOND : bond 0.01077 ( 9) SS BOND : angle 2.77349 ( 18) hydrogen bonds : bond 0.03922 ( 447) hydrogen bonds : angle 4.41781 ( 1308) link_NAG-ASN : bond 0.00449 ( 5) link_NAG-ASN : angle 2.46362 ( 15) *********************** 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 94 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8406 (pm20) cc_final: 0.7887 (tp30) REVERT: A 212 LEU cc_start: 0.8824 (mt) cc_final: 0.7833 (mp) REVERT: A 582 TYR cc_start: 0.6481 (OUTLIER) cc_final: 0.5857 (t80) REVERT: A 693 LEU cc_start: 0.9302 (mp) cc_final: 0.8826 (pp) REVERT: A 846 PHE cc_start: 0.7964 (m-10) cc_final: 0.6898 (p90) REVERT: A 986 MET cc_start: 0.8836 (tpp) cc_final: 0.8634 (tpp) REVERT: A 998 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8384 (mm) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.0568 time to fit residues: 8.2287 Evaluate side-chains 89 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 583 THR 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 998 LEU Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1127 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 46 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.121031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.092155 restraints weight = 26542.407| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.59 r_work: 0.3282 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8181 Z= 0.116 Angle : 0.628 16.043 11220 Z= 0.298 Chirality : 0.039 0.243 1306 Planarity : 0.004 0.046 1316 Dihedral : 8.534 59.593 2094 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.60 % Allowed : 14.13 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.50 (0.28), residues: 921 helix: 1.75 (0.22), residues: 566 sheet: 0.29 (1.03), residues: 26 loop : -0.22 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.018 0.001 TYR A 388 PHE 0.014 0.001 PHE A 495 TRP 0.032 0.001 TRP A 650 HIS 0.002 0.000 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8167) covalent geometry : angle 0.61412 (11187) SS BOND : bond 0.01064 ( 9) SS BOND : angle 2.55692 ( 18) hydrogen bonds : bond 0.03537 ( 447) hydrogen bonds : angle 4.32292 ( 1308) link_NAG-ASN : bond 0.00520 ( 5) link_NAG-ASN : angle 2.35800 ( 15) *********************** 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: 12 poor density : 86 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8347 (pm20) cc_final: 0.7882 (tp30) REVERT: A 212 LEU cc_start: 0.8797 (mt) cc_final: 0.7848 (mp) REVERT: A 452 MET cc_start: 0.8908 (tpp) cc_final: 0.8513 (tpt) REVERT: A 531 MET cc_start: 0.8550 (tpp) cc_final: 0.8231 (mmt) REVERT: A 582 TYR cc_start: 0.6284 (OUTLIER) cc_final: 0.5814 (t80) REVERT: A 693 LEU cc_start: 0.9285 (mp) cc_final: 0.8825 (pp) REVERT: A 771 MET cc_start: 0.7889 (mmm) cc_final: 0.7659 (mmm) REVERT: A 846 PHE cc_start: 0.7915 (m-10) cc_final: 0.6742 (p90) REVERT: A 998 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8444 (mm) outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 0.0600 time to fit residues: 8.8718 Evaluate side-chains 90 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1099 THR 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 53 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.120558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.090495 restraints weight = 31577.528| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 4.00 r_work: 0.3248 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 8181 Z= 0.124 Angle : 0.644 16.697 11220 Z= 0.305 Chirality : 0.040 0.241 1306 Planarity : 0.004 0.045 1316 Dihedral : 8.514 59.592 2094 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.23 % Allowed : 14.86 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.53 (0.28), residues: 921 helix: 1.78 (0.22), residues: 566 sheet: 0.44 (1.06), residues: 26 loop : -0.23 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 262 TYR 0.018 0.001 TYR A 388 PHE 0.014 0.001 PHE A 435 TRP 0.031 0.001 TRP A 650 HIS 0.002 0.000 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8167) covalent geometry : angle 0.63104 (11187) SS BOND : bond 0.00962 ( 9) SS BOND : angle 2.57319 ( 18) hydrogen bonds : bond 0.03608 ( 447) hydrogen bonds : angle 4.33083 ( 1308) link_NAG-ASN : bond 0.00460 ( 5) link_NAG-ASN : angle 2.30800 ( 15) *********************** 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 90 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8400 (pm20) cc_final: 0.7895 (tp30) REVERT: A 212 LEU cc_start: 0.8799 (mt) cc_final: 0.7862 (mp) REVERT: A 531 MET cc_start: 0.8581 (tpp) cc_final: 0.8273 (mmt) REVERT: A 582 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.5831 (t80) REVERT: A 693 LEU cc_start: 0.9285 (mp) cc_final: 0.8833 (pp) REVERT: A 771 MET cc_start: 0.7952 (mmm) cc_final: 0.7731 (mmm) REVERT: A 846 PHE cc_start: 0.7872 (m-10) cc_final: 0.6718 (p90) REVERT: A 869 TYR cc_start: 0.9041 (p90) cc_final: 0.8666 (m-10) REVERT: A 998 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8363 (mm) REVERT: A 1094 MET cc_start: 0.9267 (tpp) cc_final: 0.8977 (ttm) outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.0563 time to fit residues: 8.0825 Evaluate side-chains 85 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 696 VAL 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 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.119562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.089201 restraints weight = 36312.706| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.26 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 8181 Z= 0.138 Angle : 0.658 17.122 11220 Z= 0.313 Chirality : 0.040 0.241 1306 Planarity : 0.004 0.045 1316 Dihedral : 8.570 58.664 2094 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.47 % Allowed : 14.62 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.52 (0.28), residues: 921 helix: 1.75 (0.22), residues: 569 sheet: 0.48 (1.11), residues: 26 loop : -0.22 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 262 TYR 0.018 0.001 TYR A 388 PHE 0.016 0.001 PHE A 495 TRP 0.030 0.001 TRP A 650 HIS 0.002 0.001 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8167) covalent geometry : angle 0.64523 (11187) SS BOND : bond 0.00976 ( 9) SS BOND : angle 2.56163 ( 18) hydrogen bonds : bond 0.03728 ( 447) hydrogen bonds : angle 4.34697 ( 1308) link_NAG-ASN : bond 0.00452 ( 5) link_NAG-ASN : angle 2.25961 ( 15) ********************** 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 87 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8080 (pm20) cc_final: 0.7749 (tp30) REVERT: A 212 LEU cc_start: 0.8770 (mt) cc_final: 0.7776 (mp) REVERT: A 245 TYR cc_start: 0.7943 (t80) cc_final: 0.7742 (t80) REVERT: A 531 MET cc_start: 0.8429 (tpp) cc_final: 0.8120 (mmt) REVERT: A 582 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.5872 (t80) REVERT: A 693 LEU cc_start: 0.9305 (mp) cc_final: 0.8857 (pp) REVERT: A 771 MET cc_start: 0.7577 (mmm) cc_final: 0.7362 (mmm) REVERT: A 846 PHE cc_start: 0.7686 (m-10) cc_final: 0.6691 (p90) REVERT: A 869 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.8657 (m-10) REVERT: A 998 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8202 (mm) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.0546 time to fit residues: 7.4057 Evaluate side-chains 86 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 583 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 869 TYR 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 1 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 62 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.120369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090993 restraints weight = 28454.534| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.77 r_work: 0.3264 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8181 Z= 0.120 Angle : 0.643 16.963 11220 Z= 0.305 Chirality : 0.040 0.242 1306 Planarity : 0.004 0.046 1316 Dihedral : 8.475 58.357 2094 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.47 % Allowed : 14.62 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.56 (0.28), residues: 921 helix: 1.79 (0.22), residues: 567 sheet: 0.47 (1.11), residues: 26 loop : -0.21 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 262 TYR 0.017 0.001 TYR A 388 PHE 0.013 0.001 PHE A 435 TRP 0.029 0.001 TRP A 650 HIS 0.002 0.000 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8167) covalent geometry : angle 0.63110 (11187) SS BOND : bond 0.01002 ( 9) SS BOND : angle 2.47485 ( 18) hydrogen bonds : bond 0.03561 ( 447) hydrogen bonds : angle 4.32709 ( 1308) link_NAG-ASN : bond 0.00481 ( 5) link_NAG-ASN : angle 2.20976 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2005.94 seconds wall clock time: 35 minutes 1.43 seconds (2101.43 seconds total)