Starting phenix.real_space_refine on Thu Sep 10 23:22:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xwm_67337/09_2026/9xwm_67337.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xwm_67337/09_2026/9xwm_67337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xwm_67337/09_2026/9xwm_67337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xwm_67337/09_2026/9xwm_67337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xwm_67337/09_2026/9xwm_67337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xwm_67337/09_2026/9xwm_67337.map" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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 30 5.16 5 C 3228 2.51 5 N 851 2.21 5 O 1029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5138 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Chain: "D" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "E" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 892 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.14, per 1000 atoms: 0.22 Number of scatterers: 5138 At special positions: 0 Unit cell: (71.34, 81.18, 112.34, 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 30 16.00 O 1029 8.00 N 851 7.00 C 3228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 396 " distance=2.03 Simple disulfide: pdb=" SG CYS A 414 " - pdb=" SG CYS A 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 426 " - pdb=" SG CYS A 572 " distance=2.04 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 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 A 601 " - " ASN A 387 " " NAG A 602 " - " ASN A 399 " " NAG A 603 " - " ASN A 482 " Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 128.0 milliseconds 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1212 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 15 sheets defined 10.5% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.545A pdb=" N LEU A 377 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 438 through 442 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 512 through 520 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.717A pdb=" N THR B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.711A pdb=" N LEU D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.782A pdb=" N THR E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.688A pdb=" N SER E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 435 removed outlier: 3.620A pdb=" N SER A 429 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 560 " --> pdb=" O CYS A 467 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 435 removed outlier: 3.620A pdb=" N SER A 429 " --> pdb=" O ASN A 563 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 490 through 494 removed outlier: 6.003A pdb=" N GLY A 541 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.835A pdb=" N CYS C 22 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 83 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 18 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.835A pdb=" N CYS C 22 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.034A pdb=" N GLU C 10 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.034A pdb=" N GLU C 10 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR C 108 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.729A pdb=" N ALA B 19 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 75 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.383A pdb=" N MET B 37 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TYR B 53 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP B 39 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.704A pdb=" N GLN B 94 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR B 101 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 5 removed outlier: 4.385A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER D 67 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.579A pdb=" N MET D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA D 84 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.579A pdb=" N MET D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA D 84 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.638A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET E 20 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET E 81 " --> pdb=" O MET E 20 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.927A pdb=" N GLU E 10 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) 155 hydrogen bonds defined for protein. 375 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: 0.64 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1437 1.33 - 1.45: 1068 1.45 - 1.57: 2706 1.57 - 1.70: 1 1.70 - 1.82: 44 Bond restraints: 5256 Sorted by residual: bond pdb=" N CYS A 572 " pdb=" CA CYS A 572 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.85e+01 bond pdb=" CA SER A 428 " pdb=" CB SER A 428 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.69e-02 3.50e+03 1.03e+01 bond pdb=" N VAL A 409 " pdb=" CA VAL A 409 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.95e+00 bond pdb=" C PRO B 47 " pdb=" O PRO B 47 " ideal model delta sigma weight residual 1.243 1.217 0.026 8.50e-03 1.38e+04 9.69e+00 bond pdb=" N VAL A 407 " pdb=" CA VAL A 407 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.54e+00 ... (remaining 5251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 7059 3.18 - 6.35: 73 6.35 - 9.53: 7 9.53 - 12.71: 1 12.71 - 15.88: 1 Bond angle restraints: 7141 Sorted by residual: angle pdb=" C THR E 31 " pdb=" CA THR E 31 " pdb=" CB THR E 31 " ideal model delta sigma weight residual 109.67 93.79 15.88 2.01e+00 2.48e-01 6.24e+01 angle pdb=" N LEU A 377 " pdb=" CA LEU A 377 " pdb=" C LEU A 377 " ideal model delta sigma weight residual 113.15 104.75 8.40 1.19e+00 7.06e-01 4.99e+01 angle pdb=" CA PRO D 59 " pdb=" N PRO D 59 " pdb=" CD PRO D 59 " ideal model delta sigma weight residual 112.00 104.34 7.66 1.40e+00 5.10e-01 2.99e+01 angle pdb=" C LYS A 379 " pdb=" CA LYS A 379 " pdb=" CB LYS A 379 " ideal model delta sigma weight residual 110.42 100.30 10.12 1.99e+00 2.53e-01 2.59e+01 angle pdb=" CA PHE A 378 " pdb=" C PHE A 378 " pdb=" O PHE A 378 " ideal model delta sigma weight residual 120.21 114.05 6.16 1.35e+00 5.49e-01 2.09e+01 ... (remaining 7136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 2720 16.93 - 33.85: 330 33.85 - 50.78: 75 50.78 - 67.70: 23 67.70 - 84.63: 5 Dihedral angle restraints: 3153 sinusoidal: 1244 harmonic: 1909 Sorted by residual: dihedral pdb=" C THR E 31 " pdb=" N THR E 31 " pdb=" CA THR E 31 " pdb=" CB THR E 31 " ideal model delta harmonic sigma weight residual -122.00 -104.98 -17.02 0 2.50e+00 1.60e-01 4.63e+01 dihedral pdb=" CB CYS A 372 " pdb=" SG CYS A 372 " pdb=" SG CYS A 396 " pdb=" CB CYS A 396 " ideal model delta sinusoidal sigma weight residual 93.00 34.40 58.60 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CB CYS A 426 " pdb=" SG CYS A 426 " pdb=" SG CYS A 572 " pdb=" CB CYS A 572 " ideal model delta sinusoidal sigma weight residual -86.00 -39.14 -46.86 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 3150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 666 0.078 - 0.156: 103 0.156 - 0.234: 13 0.234 - 0.312: 3 0.312 - 0.390: 1 Chirality restraints: 786 Sorted by residual: chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 399 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA LYS A 379 " pdb=" N LYS A 379 " pdb=" C LYS A 379 " pdb=" CB LYS A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA TYR A 564 " pdb=" N TYR A 564 " pdb=" C TYR A 564 " pdb=" CB TYR A 564 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 783 not shown) Planarity restraints: 925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 58 " -0.087 5.00e-02 4.00e+02 1.27e-01 2.56e+01 pdb=" N PRO D 59 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 561 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C THR A 561 " -0.034 2.00e-02 2.50e+03 pdb=" O THR A 561 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 562 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 52 " -0.033 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO C 53 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.026 5.00e-02 4.00e+02 ... (remaining 922 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 143 2.67 - 3.22: 4693 3.22 - 3.78: 7458 3.78 - 4.34: 10152 4.34 - 4.90: 17114 Nonbonded interactions: 39560 Sorted by model distance: nonbonded pdb=" OH TYR A 388 " pdb=" O ASN A 457 " model vdw 2.107 3.040 nonbonded pdb=" OE1 GLN D 6 " pdb=" OG1 THR D 102 " model vdw 2.163 3.040 nonbonded pdb=" OE2 GLU A 420 " pdb=" OH TYR D 94 " model vdw 2.190 3.040 nonbonded pdb=" OE2 GLU E 6 " pdb=" OG1 THR E 109 " model vdw 2.193 3.040 nonbonded pdb=" NH2 ARG A 494 " pdb=" OD2 ASP A 527 " model vdw 2.258 3.120 ... (remaining 39555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.070 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 5.670 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.006 0.101 5267 Z= 0.407 Angle : 0.920 15.883 7166 Z= 0.574 Chirality : 0.058 0.390 786 Planarity : 0.006 0.127 922 Dihedral : 15.851 84.626 1917 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.92 % Favored : 90.46 % Rotamer: Outliers : 0.90 % Allowed : 23.66 % Favored : 75.45 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 14.81 % 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: -1.64 (0.33), residues: 650 helix: -1.56 (1.03), residues: 24 sheet: -0.89 (0.32), residues: 261 loop : -1.16 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 13 TYR 0.025 0.002 TYR A 564 PHE 0.029 0.002 PHE D 71 TRP 0.020 0.002 TRP D 92 HIS 0.007 0.002 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.41 ( 5256) covalent geometry : angle 0.91171 / 0.57 ( 7141) SS BOND : bond 0.00354 / 0.21 ( 8) SS BOND : angle 1.22033 / 0.69 ( 16) hydrogen bonds : bond 0.25476 / 16.52 ( 139) hydrogen bonds : angle 10.67494 / 7.15 ( 375) link_NAG-ASN : bond 0.00317 / 0.15 ( 3) link_NAG-ASN : angle 3.39406 / 2.02 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 185 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 408 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7885 (mm-30) REVERT: A 442 LYS cc_start: 0.8912 (pttt) cc_final: 0.8620 (pttm) REVERT: A 449 SER cc_start: 0.8837 (t) cc_final: 0.8598 (p) REVERT: A 509 GLN cc_start: 0.8557 (mm110) cc_final: 0.8346 (mt0) REVERT: B 4 MET cc_start: 0.8067 (mmm) cc_final: 0.7783 (tpt) REVERT: B 32 TYR cc_start: 0.8088 (m-80) cc_final: 0.7266 (m-80) REVERT: E 10 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7580 (mp0) outliers start: 5 outliers final: 3 residues processed: 190 average time/residue: 0.0650 time to fit residues: 16.1111 Evaluate side-chains 173 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain E residue 31 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 0.0570 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 ASN A 570 ASN C 43 GLN C 82 GLN E 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129854 restraints weight = 7509.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133726 restraints weight = 3961.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136333 restraints weight = 2519.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138112 restraints weight = 1791.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139437 restraints weight = 1371.118| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 5267 Z= 0.158 Angle : 0.701 8.612 7166 Z= 0.370 Chirality : 0.048 0.308 786 Planarity : 0.005 0.076 922 Dihedral : 6.084 54.168 789 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.46 % Favored : 91.23 % Rotamer: Outliers : 4.84 % Allowed : 24.91 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: -1.53 (0.32), residues: 650 helix: -1.51 (0.87), residues: 32 sheet: -0.85 (0.31), residues: 265 loop : -1.02 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 13 TYR 0.028 0.002 TYR C 105 PHE 0.015 0.002 PHE E 29 TRP 0.012 0.002 TRP A 434 HIS 0.007 0.002 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 5256) covalent geometry : angle 0.68510 / 0.37 ( 7141) SS BOND : bond 0.00377 / 0.20 ( 8) SS BOND : angle 1.71217 / 0.93 ( 16) hydrogen bonds : bond 0.04136 / 2.68 ( 139) hydrogen bonds : angle 6.98692 / 4.62 ( 375) link_NAG-ASN : bond 0.00432 / 0.21 ( 3) link_NAG-ASN : angle 3.62105 / 1.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 LYS cc_start: 0.7150 (ptmm) cc_final: 0.6640 (mmtt) REVERT: A 412 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.8010 (m-10) REVERT: A 441 MET cc_start: 0.8173 (pmm) cc_final: 0.7954 (ptp) REVERT: A 442 LYS cc_start: 0.8818 (pttt) cc_final: 0.8556 (pttm) REVERT: A 509 GLN cc_start: 0.8646 (mm110) cc_final: 0.8389 (mt0) REVERT: C 65 LYS cc_start: 0.8965 (tppt) cc_final: 0.8680 (tptp) REVERT: B 32 TYR cc_start: 0.7926 (m-80) cc_final: 0.7506 (m-80) REVERT: D 49 TYR cc_start: 0.8279 (p90) cc_final: 0.8038 (p90) REVERT: E 10 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7757 (mp0) REVERT: E 60 TYR cc_start: 0.9071 (m-80) cc_final: 0.8807 (m-80) outliers start: 27 outliers final: 16 residues processed: 181 average time/residue: 0.0588 time to fit residues: 13.8508 Evaluate side-chains 180 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 2 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 43 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126818 restraints weight = 7528.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130607 restraints weight = 4006.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133230 restraints weight = 2563.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135028 restraints weight = 1825.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136234 restraints weight = 1400.302| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5267 Z= 0.178 Angle : 0.687 9.620 7166 Z= 0.358 Chirality : 0.047 0.315 786 Planarity : 0.005 0.061 922 Dihedral : 5.754 64.328 785 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.77 % Favored : 90.92 % Rotamer: Outliers : 5.20 % Allowed : 26.16 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: -1.40 (0.33), residues: 650 helix: -1.45 (0.86), residues: 32 sheet: -0.73 (0.32), residues: 266 loop : -0.97 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 13 TYR 0.019 0.002 TYR A 427 PHE 0.022 0.002 PHE D 71 TRP 0.012 0.002 TRP A 434 HIS 0.005 0.002 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 5256) covalent geometry : angle 0.66932 / 0.35 ( 7141) SS BOND : bond 0.00269 / 0.15 ( 8) SS BOND : angle 1.87863 / 1.00 ( 16) hydrogen bonds : bond 0.03857 / 2.49 ( 139) hydrogen bonds : angle 6.44842 / 4.21 ( 375) link_NAG-ASN : bond 0.00409 / 0.20 ( 3) link_NAG-ASN : angle 3.74684 / 1.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 379 LYS cc_start: 0.7067 (ptmm) cc_final: 0.6627 (mmtt) REVERT: A 442 LYS cc_start: 0.8820 (pttt) cc_final: 0.8549 (pttm) REVERT: A 494 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.7377 (ttp80) REVERT: A 509 GLN cc_start: 0.8644 (mm110) cc_final: 0.8395 (mt0) REVERT: C 65 LYS cc_start: 0.9016 (tppt) cc_final: 0.8805 (tptp) REVERT: C 111 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8002 (mt0) REVERT: B 4 MET cc_start: 0.7659 (mmm) cc_final: 0.7203 (ttm) REVERT: B 32 TYR cc_start: 0.7861 (m-80) cc_final: 0.7558 (m-80) REVERT: B 46 GLN cc_start: 0.8011 (mt0) cc_final: 0.7657 (tt0) REVERT: D 49 TYR cc_start: 0.8456 (p90) cc_final: 0.8241 (p90) REVERT: D 93 ASN cc_start: 0.7850 (t0) cc_final: 0.7513 (t0) REVERT: E 10 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7823 (mp0) REVERT: E 60 TYR cc_start: 0.9059 (m-80) cc_final: 0.8805 (m-80) outliers start: 29 outliers final: 18 residues processed: 182 average time/residue: 0.0791 time to fit residues: 18.5008 Evaluate side-chains 176 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN B 94 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127467 restraints weight = 7511.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131225 restraints weight = 4070.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133874 restraints weight = 2620.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135667 restraints weight = 1873.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136837 restraints weight = 1442.558| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5267 Z= 0.156 Angle : 0.674 9.415 7166 Z= 0.348 Chirality : 0.047 0.312 786 Planarity : 0.005 0.058 922 Dihedral : 5.532 62.002 785 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.85 % Favored : 92.00 % Rotamer: Outliers : 6.27 % Allowed : 24.55 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 (0.33), residues: 650 helix: -1.20 (0.88), residues: 32 sheet: -0.65 (0.32), residues: 265 loop : -0.83 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 40 TYR 0.016 0.002 TYR D 49 PHE 0.025 0.002 PHE D 71 TRP 0.011 0.001 TRP A 434 HIS 0.004 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 5256) covalent geometry : angle 0.65504 / 0.34 ( 7141) SS BOND : bond 0.00512 / 0.27 ( 8) SS BOND : angle 1.88252 / 1.05 ( 16) hydrogen bonds : bond 0.03468 / 2.24 ( 139) hydrogen bonds : angle 6.05930 / 3.94 ( 375) link_NAG-ASN : bond 0.00474 / 0.23 ( 3) link_NAG-ASN : angle 3.81940 / 1.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.8855 (pttt) cc_final: 0.8462 (pttm) REVERT: A 489 TYR cc_start: 0.7431 (m-80) cc_final: 0.6832 (m-80) REVERT: A 509 GLN cc_start: 0.8611 (mm110) cc_final: 0.8353 (mt0) REVERT: C 65 LYS cc_start: 0.9048 (tppt) cc_final: 0.8843 (tptp) REVERT: C 81 MET cc_start: 0.8517 (ttt) cc_final: 0.8276 (ttt) REVERT: C 111 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7953 (mt0) REVERT: B 6 GLN cc_start: 0.8501 (tt0) cc_final: 0.8300 (tt0) REVERT: B 31 ASN cc_start: 0.8658 (t0) cc_final: 0.8343 (t0) REVERT: D 49 TYR cc_start: 0.8557 (p90) cc_final: 0.8293 (p90) REVERT: E 10 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7840 (mp0) outliers start: 35 outliers final: 22 residues processed: 183 average time/residue: 0.0698 time to fit residues: 16.6984 Evaluate side-chains 177 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 13 optimal weight: 0.0010 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 0.0570 chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 53 optimal weight: 0.0970 overall best weight: 0.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 43 GLN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN E 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131514 restraints weight = 7580.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135523 restraints weight = 4056.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.138284 restraints weight = 2582.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140167 restraints weight = 1822.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.141458 restraints weight = 1385.484| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 5267 Z= 0.110 Angle : 0.632 8.880 7166 Z= 0.327 Chirality : 0.045 0.288 786 Planarity : 0.004 0.053 922 Dihedral : 5.107 65.396 785 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.31 % Favored : 93.54 % Rotamer: Outliers : 3.41 % Allowed : 28.32 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: -1.00 (0.33), residues: 650 helix: -0.72 (0.93), residues: 33 sheet: -0.35 (0.32), residues: 251 loop : -0.83 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 65 TYR 0.023 0.001 TYR B 32 PHE 0.024 0.001 PHE D 71 TRP 0.012 0.001 TRP C 47 HIS 0.003 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 5256) covalent geometry : angle 0.61646 / 0.32 ( 7141) SS BOND : bond 0.00362 / 0.19 ( 8) SS BOND : angle 1.36109 / 0.80 ( 16) hydrogen bonds : bond 0.02949 / 1.91 ( 139) hydrogen bonds : angle 5.64842 / 3.66 ( 375) link_NAG-ASN : bond 0.00612 / 0.29 ( 3) link_NAG-ASN : angle 3.62262 / 1.71 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 LYS cc_start: 0.8722 (pttt) cc_final: 0.8057 (pttm) REVERT: A 417 THR cc_start: 0.9356 (t) cc_final: 0.9056 (m) REVERT: A 442 LYS cc_start: 0.8812 (pttt) cc_final: 0.8444 (pttm) REVERT: A 489 TYR cc_start: 0.7309 (m-80) cc_final: 0.6508 (m-80) REVERT: A 509 GLN cc_start: 0.8533 (mm110) cc_final: 0.8275 (mt0) REVERT: C 63 LYS cc_start: 0.7986 (ptmm) cc_final: 0.7667 (pptt) REVERT: C 65 LYS cc_start: 0.9018 (tppt) cc_final: 0.8767 (tptp) REVERT: C 111 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7952 (mt0) REVERT: D 49 TYR cc_start: 0.8420 (p90) cc_final: 0.8027 (p90) REVERT: E 10 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7797 (mp0) outliers start: 19 outliers final: 11 residues processed: 176 average time/residue: 0.0737 time to fit residues: 16.8120 Evaluate side-chains 165 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 43 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122114 restraints weight = 7797.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126015 restraints weight = 4155.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.128771 restraints weight = 2652.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130585 restraints weight = 1872.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131849 restraints weight = 1434.170| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5267 Z= 0.197 Angle : 0.695 9.802 7166 Z= 0.360 Chirality : 0.047 0.289 786 Planarity : 0.005 0.053 922 Dihedral : 5.318 57.052 785 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.92 % Favored : 90.92 % Rotamer: Outliers : 6.81 % Allowed : 24.91 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: -1.08 (0.34), residues: 650 helix: -0.89 (0.93), residues: 32 sheet: -0.50 (0.32), residues: 269 loop : -0.78 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.019 0.002 TYR B 32 PHE 0.012 0.002 PHE D 71 TRP 0.009 0.002 TRP A 434 HIS 0.004 0.002 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 ( 5256) covalent geometry : angle 0.67868 / 0.36 ( 7141) SS BOND : bond 0.00367 / 0.20 ( 8) SS BOND : angle 1.80085 / 1.02 ( 16) hydrogen bonds : bond 0.03439 / 2.22 ( 139) hydrogen bonds : angle 5.74314 / 3.73 ( 375) link_NAG-ASN : bond 0.00279 / 0.13 ( 3) link_NAG-ASN : angle 3.64219 / 1.67 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 416 LYS cc_start: 0.8853 (pttt) cc_final: 0.8511 (ptpt) REVERT: A 442 LYS cc_start: 0.8852 (pttt) cc_final: 0.8441 (pttm) REVERT: A 489 TYR cc_start: 0.7554 (m-80) cc_final: 0.6889 (m-80) REVERT: A 509 GLN cc_start: 0.8656 (mm110) cc_final: 0.8379 (mt0) REVERT: C 65 LYS cc_start: 0.9108 (tppt) cc_final: 0.8867 (tptp) REVERT: C 81 MET cc_start: 0.8593 (ttt) cc_final: 0.8334 (ttt) REVERT: C 111 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8013 (mt0) REVERT: D 49 TYR cc_start: 0.8644 (p90) cc_final: 0.8402 (p90) REVERT: E 10 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7819 (mp0) outliers start: 38 outliers final: 29 residues processed: 192 average time/residue: 0.0691 time to fit residues: 17.0360 Evaluate side-chains 188 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.0070 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.0170 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 0.0670 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN B 6 GLN B 78 ASN B 94 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127260 restraints weight = 7700.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131170 restraints weight = 4085.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133899 restraints weight = 2601.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135740 restraints weight = 1839.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137130 restraints weight = 1408.891| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5267 Z= 0.118 Angle : 0.659 9.423 7166 Z= 0.340 Chirality : 0.045 0.286 786 Planarity : 0.005 0.073 922 Dihedral : 5.071 60.757 785 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.15 % Favored : 93.69 % Rotamer: Outliers : 4.66 % Allowed : 27.96 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: -1.01 (0.33), residues: 650 helix: -0.64 (0.96), residues: 32 sheet: -0.24 (0.33), residues: 245 loop : -0.94 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 40 TYR 0.015 0.001 TYR D 49 PHE 0.013 0.001 PHE A 538 TRP 0.011 0.001 TRP C 47 HIS 0.003 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5256) covalent geometry : angle 0.64308 / 0.34 ( 7141) SS BOND : bond 0.00393 / 0.20 ( 8) SS BOND : angle 1.55226 / 0.93 ( 16) hydrogen bonds : bond 0.02944 / 1.93 ( 139) hydrogen bonds : angle 5.51088 / 3.57 ( 375) link_NAG-ASN : bond 0.00508 / 0.24 ( 3) link_NAG-ASN : angle 3.62225 / 1.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.8829 (pttt) cc_final: 0.8464 (pttm) REVERT: A 489 TYR cc_start: 0.7501 (m-80) cc_final: 0.6818 (m-80) REVERT: A 509 GLN cc_start: 0.8629 (mm110) cc_final: 0.8333 (mt0) REVERT: A 563 ASN cc_start: 0.8522 (m-40) cc_final: 0.8232 (p0) REVERT: C 65 LYS cc_start: 0.9061 (tppt) cc_final: 0.8841 (tptp) REVERT: C 81 MET cc_start: 0.8475 (ttt) cc_final: 0.8226 (ttt) REVERT: C 111 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7978 (mt0) REVERT: B 5 THR cc_start: 0.8611 (m) cc_final: 0.8375 (t) REVERT: D 49 TYR cc_start: 0.8566 (p90) cc_final: 0.8258 (p90) REVERT: E 10 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7828 (mp0) outliers start: 26 outliers final: 22 residues processed: 169 average time/residue: 0.0715 time to fit residues: 15.6500 Evaluate side-chains 171 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN B 6 GLN B 94 GLN D 6 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.138312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121140 restraints weight = 7832.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124847 restraints weight = 4183.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127474 restraints weight = 2688.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.129303 restraints weight = 1921.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130510 restraints weight = 1473.645| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5267 Z= 0.217 Angle : 0.741 11.267 7166 Z= 0.382 Chirality : 0.048 0.301 786 Planarity : 0.005 0.053 922 Dihedral : 5.272 45.308 785 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.38 % Favored : 90.46 % Rotamer: Outliers : 5.91 % Allowed : 25.81 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: -1.28 (0.33), residues: 650 helix: -0.93 (0.95), residues: 32 sheet: -0.65 (0.32), residues: 266 loop : -0.92 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 13 TYR 0.022 0.002 TYR B 32 PHE 0.016 0.002 PHE A 538 TRP 0.011 0.002 TRP A 434 HIS 0.004 0.002 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 ( 5256) covalent geometry : angle 0.72452 / 0.38 ( 7141) SS BOND : bond 0.00495 / 0.26 ( 8) SS BOND : angle 1.77109 / 1.00 ( 16) hydrogen bonds : bond 0.03518 / 2.28 ( 139) hydrogen bonds : angle 5.81048 / 3.79 ( 375) link_NAG-ASN : bond 0.00271 / 0.13 ( 3) link_NAG-ASN : angle 3.83372 / 1.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.8849 (pttt) cc_final: 0.8466 (pttm) REVERT: A 489 TYR cc_start: 0.7617 (m-80) cc_final: 0.6877 (m-80) REVERT: A 509 GLN cc_start: 0.8715 (mm110) cc_final: 0.8422 (mt0) REVERT: A 528 TYR cc_start: 0.6908 (t80) cc_final: 0.6656 (t80) REVERT: C 64 PHE cc_start: 0.8468 (m-10) cc_final: 0.8220 (m-10) REVERT: C 65 LYS cc_start: 0.9135 (tppt) cc_final: 0.8920 (tptp) REVERT: C 81 MET cc_start: 0.8651 (ttt) cc_final: 0.8432 (ttt) REVERT: C 111 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7974 (mt0) REVERT: B 5 THR cc_start: 0.8715 (m) cc_final: 0.8483 (t) REVERT: E 10 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7846 (mp0) outliers start: 33 outliers final: 29 residues processed: 183 average time/residue: 0.0678 time to fit residues: 16.1764 Evaluate side-chains 185 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 2 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.0040 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 43 GLN B 94 GLN D 91 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123082 restraints weight = 7763.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126859 restraints weight = 4132.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.129504 restraints weight = 2650.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131384 restraints weight = 1891.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132681 restraints weight = 1443.975| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5267 Z= 0.167 Angle : 0.731 10.845 7166 Z= 0.374 Chirality : 0.047 0.286 786 Planarity : 0.005 0.053 922 Dihedral : 5.164 46.920 785 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.77 % Favored : 93.08 % Rotamer: Outliers : 5.20 % Allowed : 28.14 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: -1.28 (0.33), residues: 650 helix: -1.07 (0.93), residues: 32 sheet: -0.39 (0.34), residues: 250 loop : -1.13 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 40 TYR 0.019 0.002 TYR D 49 PHE 0.014 0.002 PHE A 538 TRP 0.010 0.001 TRP C 47 HIS 0.004 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 5256) covalent geometry : angle 0.71502 / 0.37 ( 7141) SS BOND : bond 0.00480 / 0.25 ( 8) SS BOND : angle 1.73843 / 1.03 ( 16) hydrogen bonds : bond 0.03358 / 2.16 ( 139) hydrogen bonds : angle 5.64121 / 3.65 ( 375) link_NAG-ASN : bond 0.00253 / 0.12 ( 3) link_NAG-ASN : angle 3.77225 / 1.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.8823 (pttt) cc_final: 0.8480 (pttm) REVERT: A 489 TYR cc_start: 0.7631 (m-80) cc_final: 0.6926 (m-80) REVERT: A 509 GLN cc_start: 0.8707 (mm110) cc_final: 0.8407 (mt0) REVERT: C 81 MET cc_start: 0.8559 (ttt) cc_final: 0.8235 (ttt) REVERT: C 111 GLN cc_start: 0.8387 (mm-40) cc_final: 0.7966 (mt0) REVERT: E 10 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7883 (mp0) outliers start: 29 outliers final: 25 residues processed: 177 average time/residue: 0.0739 time to fit residues: 16.8328 Evaluate side-chains 182 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN B 78 ASN B 94 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120186 restraints weight = 8021.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123194 restraints weight = 4699.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125316 restraints weight = 3164.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126741 restraints weight = 2318.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127858 restraints weight = 1813.498| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5267 Z= 0.173 Angle : 0.738 11.437 7166 Z= 0.375 Chirality : 0.047 0.285 786 Planarity : 0.005 0.053 922 Dihedral : 5.227 48.600 785 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.77 % Favored : 91.08 % Rotamer: Outliers : 5.02 % Allowed : 28.85 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: -1.30 (0.33), residues: 650 helix: -1.23 (0.93), residues: 32 sheet: -0.41 (0.34), residues: 248 loop : -1.13 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 40 TYR 0.022 0.002 TYR B 32 PHE 0.019 0.002 PHE C 64 TRP 0.010 0.001 TRP C 47 HIS 0.004 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 5256) covalent geometry : angle 0.72263 / 0.37 ( 7141) SS BOND : bond 0.00426 / 0.22 ( 8) SS BOND : angle 1.72199 / 1.01 ( 16) hydrogen bonds : bond 0.03365 / 2.18 ( 139) hydrogen bonds : angle 5.66842 / 3.70 ( 375) link_NAG-ASN : bond 0.00344 / 0.16 ( 3) link_NAG-ASN : angle 3.77026 / 1.76 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.8784 (pttt) cc_final: 0.8404 (pttm) REVERT: A 489 TYR cc_start: 0.7593 (m-80) cc_final: 0.6867 (m-80) REVERT: A 509 GLN cc_start: 0.8777 (mm110) cc_final: 0.8411 (mt0) REVERT: C 111 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8026 (mt0) REVERT: E 10 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7886 (mp0) outliers start: 28 outliers final: 26 residues processed: 173 average time/residue: 0.0703 time to fit residues: 15.8580 Evaluate side-chains 180 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 TYR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 488 ASN C 43 GLN B 6 GLN B 94 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122176 restraints weight = 7956.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125381 restraints weight = 4580.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127647 restraints weight = 3040.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129127 restraints weight = 2196.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.130334 restraints weight = 1710.738| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5267 Z= 0.146 Angle : 0.731 10.804 7166 Z= 0.374 Chirality : 0.047 0.282 786 Planarity : 0.005 0.056 922 Dihedral : 5.037 47.920 785 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.15 % Favored : 93.69 % Rotamer: Outliers : 5.02 % Allowed : 29.39 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: -1.23 (0.33), residues: 650 helix: -1.10 (0.94), residues: 32 sheet: -0.32 (0.34), residues: 246 loop : -1.12 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 40 TYR 0.019 0.001 TYR D 49 PHE 0.014 0.001 PHE C 64 TRP 0.014 0.001 TRP C 47 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 5256) covalent geometry : angle 0.71554 / 0.37 ( 7141) SS BOND : bond 0.00411 / 0.22 ( 8) SS BOND : angle 1.60553 / 0.94 ( 16) hydrogen bonds : bond 0.03136 / 2.02 ( 139) hydrogen bonds : angle 5.54998 / 3.62 ( 375) link_NAG-ASN : bond 0.00410 / 0.20 ( 3) link_NAG-ASN : angle 3.77134 / 1.80 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1059.71 seconds wall clock time: 19 minutes 22.84 seconds (1162.84 seconds total)