Starting phenix.real_space_refine on Thu Jul 2 09:53:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m42_23662/07_2026/7m42_23662.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m42_23662/07_2026/7m42_23662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m42_23662/07_2026/7m42_23662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m42_23662/07_2026/7m42_23662.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m42_23662/07_2026/7m42_23662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m42_23662/07_2026/7m42_23662.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7m42_23662/07_2026/7m42_23662.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m42_23662/07_2026/7m42_23662.cif" } resolution = 3.3 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= 0.035 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 31 5.16 5 C 5110 2.51 5 N 1362 2.21 5 O 1612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8115 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1551 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1710 Classifications: {'peptide': 224} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 210} Chain: "E" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "C" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1572 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Chain: "D" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1700 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.58, per 1000 atoms: 0.19 Number of scatterers: 8115 At special positions: 0 Unit cell: (74.8, 114.75, 148.75, 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 31 16.00 O 1612 8.00 N 1362 7.00 C 5110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 199 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 211 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG F 1 " - " ASN E 343 " Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 359.4 milliseconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 25 sheets defined 8.7% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.764A pdb=" N ASP A 84 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU A 85 " --> pdb=" O ALA A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 81 through 85' Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 185 through 192 removed outlier: 3.707A pdb=" N HIS A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.570A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 removed outlier: 4.154A pdb=" N VAL E 367 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 389 removed outlier: 4.024A pdb=" N ASN E 388 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.964A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN E 409 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 405 through 410' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'C' and resid 127 through 133 Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.619A pdb=" N TRP C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.409A pdb=" N VAL A 10 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP A 37 " --> pdb=" O MET A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.409A pdb=" N VAL A 10 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 23 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.186A pdb=" N TYR A 176 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.186A pdb=" N TYR A 176 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 159 removed outlier: 4.378A pdb=" N TRP A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.849A pdb=" N GLU B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 117 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 134 removed outlier: 6.107A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.661A pdb=" N SER B 142 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR B 145 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 164 removed outlier: 4.259A pdb=" N TYR B 204 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.822A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.725A pdb=" N VAL C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.725A pdb=" N VAL C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.253A pdb=" N TYR C 178 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.253A pdb=" N TYR C 178 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 159 through 161 removed outlier: 4.497A pdb=" N TRP C 154 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AC4, first strand: chain 'D' and resid 58 through 60 removed outlier: 4.920A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 135 through 139 removed outlier: 6.311A pdb=" N TYR D 191 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 146 through 147 removed outlier: 4.142A pdb=" N SER D 147 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR D 191 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D 192 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 166 through 169 removed outlier: 4.576A pdb=" N TYR D 209 " --> pdb=" O VAL D 226 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2583 1.34 - 1.46: 2120 1.46 - 1.58: 3581 1.58 - 1.70: 0 1.70 - 1.83: 38 Bond restraints: 8322 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" CA VAL A 53 " pdb=" C VAL A 53 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.27e-02 6.20e+03 1.25e+00 ... (remaining 8317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 11155 1.83 - 3.66: 166 3.66 - 5.49: 21 5.49 - 7.32: 4 7.32 - 9.15: 3 Bond angle restraints: 11349 Sorted by residual: angle pdb=" N PHE A 51 " pdb=" CA PHE A 51 " pdb=" C PHE A 51 " ideal model delta sigma weight residual 109.24 100.09 9.15 1.67e+00 3.59e-01 3.00e+01 angle pdb=" C ASP A 52 " pdb=" N VAL A 53 " pdb=" CA VAL A 53 " ideal model delta sigma weight residual 121.97 128.67 -6.70 1.80e+00 3.09e-01 1.38e+01 angle pdb=" N VAL A 53 " pdb=" CA VAL A 53 " pdb=" C VAL A 53 " ideal model delta sigma weight residual 109.34 116.23 -6.89 2.08e+00 2.31e-01 1.10e+01 angle pdb=" CA LEU C 97 " pdb=" CB LEU C 97 " pdb=" CG LEU C 97 " ideal model delta sigma weight residual 116.30 125.15 -8.85 3.50e+00 8.16e-02 6.39e+00 angle pdb=" CA GLU C 204 " pdb=" CB GLU C 204 " pdb=" CG GLU C 204 " ideal model delta sigma weight residual 114.10 118.75 -4.65 2.00e+00 2.50e-01 5.41e+00 ... (remaining 11344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4474 17.03 - 34.06: 344 34.06 - 51.09: 77 51.09 - 68.12: 10 68.12 - 85.15: 8 Dihedral angle restraints: 4913 sinusoidal: 1840 harmonic: 3073 Sorted by residual: dihedral pdb=" CB CYS D 155 " pdb=" SG CYS D 155 " pdb=" SG CYS D 211 " pdb=" CB CYS D 211 " ideal model delta sinusoidal sigma weight residual 93.00 44.21 48.79 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 56.19 36.81 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CB CYS C 140 " pdb=" SG CYS C 140 " pdb=" SG CYS C 199 " pdb=" CB CYS C 199 " ideal model delta sinusoidal sigma weight residual 93.00 58.27 34.73 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 4910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1044 0.052 - 0.103: 176 0.103 - 0.155: 44 0.155 - 0.206: 5 0.206 - 0.258: 2 Chirality restraints: 1271 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LYS D 221 " pdb=" N LYS D 221 " pdb=" C LYS D 221 " pdb=" CB LYS D 221 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 1268 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 97 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.69e+00 pdb=" C ALA D 97 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA D 97 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS D 98 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 343 " -0.019 2.00e-02 2.50e+03 1.79e-02 4.02e+00 pdb=" CG ASN E 343 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN E 343 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN E 343 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 163 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO D 164 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " -0.021 5.00e-02 4.00e+02 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 136 2.68 - 3.24: 7148 3.24 - 3.79: 11566 3.79 - 4.35: 15577 4.35 - 4.90: 26834 Nonbonded interactions: 61261 Sorted by model distance: nonbonded pdb=" O ASP A 52 " pdb=" N SER A 54 " model vdw 2.128 3.120 nonbonded pdb=" OG SER A 65 " pdb=" OG1 THR A 76 " model vdw 2.135 3.040 nonbonded pdb=" OG SER D 52 " pdb=" OG SER D 57 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR B 155 " pdb=" OE2 GLU B 158 " model vdw 2.217 3.040 nonbonded pdb=" O HIS A 201 " pdb=" OG SER A 204 " model vdw 2.270 3.040 ... (remaining 61256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.590 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 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 : 0.002 0.033 8337 Z= 0.104 Angle : 0.571 9.147 11382 Z= 0.300 Chirality : 0.045 0.258 1271 Planarity : 0.004 0.042 1456 Dihedral : 12.888 85.147 2923 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 1.22 % Allowed : 10.33 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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: -2.65 (0.23), residues: 1060 helix: -3.74 (0.36), residues: 72 sheet: -0.76 (0.23), residues: 438 loop : -2.36 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 355 TYR 0.019 0.001 TYR E 351 PHE 0.008 0.001 PHE C 145 TRP 0.006 0.001 TRP B 50 HIS 0.001 0.000 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 ( 8322) covalent geometry : angle 0.55731 / 0.30 (11349) SS BOND : bond 0.00221 / 0.13 ( 12) SS BOND : angle 1.93744 / 1.13 ( 24) hydrogen bonds : bond 0.12054 / 7.97 ( 290) hydrogen bonds : angle 6.64306 / 4.79 ( 870) link_BETA1-4 : bond 0.00782 / 0.40 ( 2) link_BETA1-4 : angle 2.33886 / 1.35 ( 6) link_NAG-ASN : bond 0.00325 / 0.17 ( 1) link_NAG-ASN : angle 4.71562 / 2.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.268 Fit side-chains REVERT: E 458 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8286 (mttp) REVERT: C 55 ASN cc_start: 0.8319 (m-40) cc_final: 0.8097 (m110) REVERT: C 83 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7361 (tm-30) outliers start: 11 outliers final: 3 residues processed: 136 average time/residue: 0.0641 time to fit residues: 12.7948 Evaluate side-chains 93 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 0.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN A 198 GLN E 370 ASN E 493 GLN C 16 GLN C 28 ASN C 194 HIS D 170 ASN D 186 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.170106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121990 restraints weight = 11344.887| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.77 r_work: 0.3383 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8337 Z= 0.090 Angle : 0.528 11.273 11382 Z= 0.268 Chirality : 0.043 0.172 1271 Planarity : 0.004 0.043 1456 Dihedral : 3.689 33.816 1155 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 2.89 % Allowed : 13.44 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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: -1.89 (0.24), residues: 1060 helix: -3.09 (0.43), residues: 74 sheet: -0.21 (0.24), residues: 441 loop : -1.90 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 16 TYR 0.025 0.001 TYR C 93 PHE 0.009 0.001 PHE E 377 TRP 0.007 0.001 TRP B 50 HIS 0.003 0.000 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 ( 8322) covalent geometry : angle 0.52441 / 0.27 (11349) SS BOND : bond 0.00265 / 0.17 ( 12) SS BOND : angle 0.78221 / 0.47 ( 24) hydrogen bonds : bond 0.02787 / 1.83 ( 290) hydrogen bonds : angle 5.26957 / 3.78 ( 870) link_BETA1-4 : bond 0.00528 / 0.25 ( 2) link_BETA1-4 : angle 2.12184 / 1.10 ( 6) link_NAG-ASN : bond 0.00423 / 0.22 ( 1) link_NAG-ASN : angle 2.27741 / 1.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.241 Fit side-chains REVERT: E 335 LEU cc_start: 0.5524 (OUTLIER) cc_final: 0.5133 (tt) REVERT: E 354 ASN cc_start: 0.8666 (t0) cc_final: 0.8440 (t0) REVERT: E 458 LYS cc_start: 0.9017 (mtmt) cc_final: 0.8493 (mttp) REVERT: C 83 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 190 GLN cc_start: 0.5814 (mt0) cc_final: 0.5321 (mp10) outliers start: 26 outliers final: 16 residues processed: 114 average time/residue: 0.0653 time to fit residues: 11.0486 Evaluate side-chains 102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.0010 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS C 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113842 restraints weight = 11121.222| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.66 r_work: 0.3279 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8337 Z= 0.143 Angle : 0.557 9.550 11382 Z= 0.284 Chirality : 0.044 0.189 1271 Planarity : 0.004 0.044 1456 Dihedral : 4.125 40.528 1153 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 4.11 % Allowed : 16.00 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.49 (0.24), residues: 1060 helix: -2.68 (0.48), residues: 75 sheet: 0.06 (0.24), residues: 445 loop : -1.66 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.019 0.001 TYR C 93 PHE 0.013 0.001 PHE A 93 TRP 0.013 0.001 TRP D 53 HIS 0.002 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 8322) covalent geometry : angle 0.55323 / 0.28 (11349) SS BOND : bond 0.00370 / 0.23 ( 12) SS BOND : angle 1.05213 / 0.61 ( 24) hydrogen bonds : bond 0.03048 / 2.05 ( 290) hydrogen bonds : angle 5.16200 / 3.68 ( 870) link_BETA1-4 : bond 0.00833 / 0.40 ( 2) link_BETA1-4 : angle 1.73547 / 0.94 ( 6) link_NAG-ASN : bond 0.00327 / 0.17 ( 1) link_NAG-ASN : angle 1.69619 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.280 Fit side-chains REVERT: A 56 ARG cc_start: 0.8218 (ptt-90) cc_final: 0.7911 (ptp90) REVERT: E 335 LEU cc_start: 0.5384 (OUTLIER) cc_final: 0.5029 (tt) REVERT: E 354 ASN cc_start: 0.8840 (t0) cc_final: 0.8578 (t0) REVERT: E 420 ASP cc_start: 0.8299 (m-30) cc_final: 0.8030 (m-30) REVERT: E 458 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8424 (mttp) REVERT: C 83 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7559 (tm-30) REVERT: C 93 TYR cc_start: 0.8978 (t80) cc_final: 0.8584 (t80) REVERT: C 190 GLN cc_start: 0.5998 (mt0) cc_final: 0.5511 (mp10) REVERT: D 43 LYS cc_start: 0.7843 (mmmm) cc_final: 0.7386 (mmtm) outliers start: 37 outliers final: 26 residues processed: 127 average time/residue: 0.0598 time to fit residues: 11.2115 Evaluate side-chains 118 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.163481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115291 restraints weight = 11511.080| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.69 r_work: 0.3294 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8337 Z= 0.104 Angle : 0.531 9.302 11382 Z= 0.267 Chirality : 0.043 0.175 1271 Planarity : 0.004 0.045 1456 Dihedral : 4.045 41.866 1153 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.33 % Allowed : 18.33 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.25), residues: 1060 helix: -2.62 (0.50), residues: 69 sheet: 0.24 (0.24), residues: 442 loop : -1.49 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.014 0.001 TYR C 51 PHE 0.032 0.001 PHE A 143 TRP 0.011 0.001 TRP B 50 HIS 0.002 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 8322) covalent geometry : angle 0.52875 / 0.27 (11349) SS BOND : bond 0.00325 / 0.20 ( 12) SS BOND : angle 0.83260 / 0.48 ( 24) hydrogen bonds : bond 0.02688 / 1.78 ( 290) hydrogen bonds : angle 4.95520 / 3.53 ( 870) link_BETA1-4 : bond 0.00587 / 0.29 ( 2) link_BETA1-4 : angle 1.63594 / 0.88 ( 6) link_NAG-ASN : bond 0.00264 / 0.14 ( 1) link_NAG-ASN : angle 1.54840 / 1.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.252 Fit side-chains REVERT: A 49 MET cc_start: 0.8718 (tpp) cc_final: 0.8366 (mmt) REVERT: A 56 ARG cc_start: 0.8228 (ptt-90) cc_final: 0.7805 (ptp90) REVERT: A 127 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6311 (mp0) REVERT: E 335 LEU cc_start: 0.5357 (OUTLIER) cc_final: 0.5019 (tt) REVERT: E 354 ASN cc_start: 0.8827 (t0) cc_final: 0.8573 (t0) REVERT: E 420 ASP cc_start: 0.8385 (m-30) cc_final: 0.8084 (m-30) REVERT: E 458 LYS cc_start: 0.9010 (mtmt) cc_final: 0.8440 (mttp) REVERT: C 83 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7504 (tm-30) REVERT: C 93 TYR cc_start: 0.9001 (t80) cc_final: 0.8588 (t80) REVERT: C 190 GLN cc_start: 0.5921 (mt0) cc_final: 0.5400 (mp10) REVERT: D 43 LYS cc_start: 0.7896 (mmmm) cc_final: 0.7399 (mmtm) outliers start: 30 outliers final: 23 residues processed: 118 average time/residue: 0.0725 time to fit residues: 12.6078 Evaluate side-chains 114 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 41 HIS E 394 ASN D 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106973 restraints weight = 11523.888| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.68 r_work: 0.3170 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 8337 Z= 0.285 Angle : 0.682 9.184 11382 Z= 0.353 Chirality : 0.048 0.199 1271 Planarity : 0.005 0.046 1456 Dihedral : 4.973 44.152 1153 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.64 % Favored : 92.26 % Rotamer: Outliers : 5.11 % Allowed : 18.56 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.47 (0.25), residues: 1060 helix: -2.59 (0.52), residues: 62 sheet: 0.22 (0.25), residues: 434 loop : -1.81 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 72 TYR 0.021 0.002 TYR C 101 PHE 0.018 0.002 PHE E 515 TRP 0.020 0.002 TRP D 53 HIS 0.005 0.002 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.29 ( 8322) covalent geometry : angle 0.67858 / 0.35 (11349) SS BOND : bond 0.00639 / 0.43 ( 12) SS BOND : angle 1.35970 / 0.78 ( 24) hydrogen bonds : bond 0.03749 / 2.58 ( 290) hydrogen bonds : angle 5.66667 / 4.00 ( 870) link_BETA1-4 : bond 0.00703 / 0.34 ( 2) link_BETA1-4 : angle 1.45631 / 0.84 ( 6) link_NAG-ASN : bond 0.00158 / 0.08 ( 1) link_NAG-ASN : angle 1.76507 / 1.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 92 time to evaluate : 0.311 Fit side-chains REVERT: A 188 GLN cc_start: 0.7663 (mm-40) cc_final: 0.6673 (tp-100) REVERT: E 335 LEU cc_start: 0.5420 (OUTLIER) cc_final: 0.5074 (tt) REVERT: E 354 ASN cc_start: 0.8887 (t0) cc_final: 0.8684 (t0) REVERT: E 392 PHE cc_start: 0.7232 (m-10) cc_final: 0.7029 (m-10) REVERT: E 458 LYS cc_start: 0.9010 (mtmt) cc_final: 0.8507 (mttp) REVERT: C 83 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7581 (tm-30) REVERT: C 93 TYR cc_start: 0.9106 (t80) cc_final: 0.8718 (t80) REVERT: C 97 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8854 (pp) REVERT: D 43 LYS cc_start: 0.7685 (mmmm) cc_final: 0.7248 (mmtm) REVERT: D 65 LYS cc_start: 0.8688 (tptt) cc_final: 0.8440 (tttm) REVERT: D 76 LYS cc_start: 0.8015 (mptt) cc_final: 0.7619 (mmtp) outliers start: 46 outliers final: 35 residues processed: 128 average time/residue: 0.0728 time to fit residues: 13.6890 Evaluate side-chains 121 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 85 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 0.0870 chunk 35 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.158652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110487 restraints weight = 11327.688| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.67 r_work: 0.3235 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8337 Z= 0.133 Angle : 0.582 9.216 11382 Z= 0.295 Chirality : 0.044 0.204 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.643 46.342 1153 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 3.67 % Allowed : 21.00 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.31 (0.25), residues: 1060 helix: -2.70 (0.48), residues: 75 sheet: 0.22 (0.25), residues: 446 loop : -1.56 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.029 0.001 TYR D 160 PHE 0.025 0.001 PHE A 143 TRP 0.014 0.001 TRP B 50 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8322) covalent geometry : angle 0.57922 / 0.29 (11349) SS BOND : bond 0.00409 / 0.25 ( 12) SS BOND : angle 0.96918 / 0.57 ( 24) hydrogen bonds : bond 0.02974 / 2.00 ( 290) hydrogen bonds : angle 5.34855 / 3.79 ( 870) link_BETA1-4 : bond 0.00483 / 0.24 ( 2) link_BETA1-4 : angle 1.48860 / 0.82 ( 6) link_NAG-ASN : bond 0.00141 / 0.07 ( 1) link_NAG-ASN : angle 1.64626 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.300 Fit side-chains REVERT: A 49 MET cc_start: 0.8823 (tpp) cc_final: 0.8544 (mmt) REVERT: A 188 GLN cc_start: 0.7665 (mm-40) cc_final: 0.6693 (tp-100) REVERT: E 335 LEU cc_start: 0.5410 (OUTLIER) cc_final: 0.5086 (tt) REVERT: E 354 ASN cc_start: 0.8865 (t0) cc_final: 0.8661 (t0) REVERT: E 392 PHE cc_start: 0.7254 (m-10) cc_final: 0.7034 (m-10) REVERT: E 458 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8520 (mttp) REVERT: C 83 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 93 TYR cc_start: 0.9039 (t80) cc_final: 0.8629 (t80) REVERT: D 43 LYS cc_start: 0.7664 (mmmm) cc_final: 0.7240 (mmtm) REVERT: D 65 LYS cc_start: 0.8533 (tptt) cc_final: 0.8251 (tttm) REVERT: D 76 LYS cc_start: 0.7916 (mptt) cc_final: 0.7527 (mmtp) outliers start: 33 outliers final: 30 residues processed: 106 average time/residue: 0.0712 time to fit residues: 11.1114 Evaluate side-chains 112 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.157729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110286 restraints weight = 11274.612| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.67 r_work: 0.3226 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8337 Z= 0.153 Angle : 0.590 10.313 11382 Z= 0.298 Chirality : 0.045 0.214 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.611 45.880 1153 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.32 % Favored : 93.58 % Rotamer: Outliers : 4.11 % Allowed : 21.22 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.25), residues: 1060 helix: -2.70 (0.47), residues: 75 sheet: 0.23 (0.25), residues: 446 loop : -1.53 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.028 0.001 TYR D 160 PHE 0.025 0.002 PHE A 143 TRP 0.015 0.001 TRP B 50 HIS 0.004 0.001 HIS D 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 8322) covalent geometry : angle 0.58707 / 0.30 (11349) SS BOND : bond 0.00479 / 0.32 ( 12) SS BOND : angle 1.01754 / 0.58 ( 24) hydrogen bonds : bond 0.03015 / 2.03 ( 290) hydrogen bonds : angle 5.29091 / 3.75 ( 870) link_BETA1-4 : bond 0.00570 / 0.28 ( 2) link_BETA1-4 : angle 1.39320 / 0.77 ( 6) link_NAG-ASN : bond 0.00201 / 0.11 ( 1) link_NAG-ASN : angle 1.70139 / 1.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.371 Fit side-chains REVERT: A 49 MET cc_start: 0.8815 (tpp) cc_final: 0.8500 (mmt) REVERT: A 188 GLN cc_start: 0.7667 (mm-40) cc_final: 0.6718 (tp-100) REVERT: E 335 LEU cc_start: 0.5371 (OUTLIER) cc_final: 0.5058 (tt) REVERT: E 392 PHE cc_start: 0.7267 (m-10) cc_final: 0.7059 (m-10) REVERT: E 458 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8495 (mttp) REVERT: C 83 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 93 TYR cc_start: 0.9038 (t80) cc_final: 0.8612 (t80) REVERT: D 43 LYS cc_start: 0.7655 (mmmm) cc_final: 0.7220 (mmtm) REVERT: D 65 LYS cc_start: 0.8558 (tptt) cc_final: 0.8328 (tttm) REVERT: D 76 LYS cc_start: 0.7935 (mptt) cc_final: 0.7559 (mmtp) outliers start: 37 outliers final: 33 residues processed: 107 average time/residue: 0.0728 time to fit residues: 11.3267 Evaluate side-chains 111 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 360 ASN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.154849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107644 restraints weight = 11253.488| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.61 r_work: 0.3187 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8337 Z= 0.244 Angle : 0.658 11.228 11382 Z= 0.336 Chirality : 0.047 0.208 1271 Planarity : 0.005 0.046 1456 Dihedral : 4.970 46.090 1153 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.45 % Favored : 92.45 % Rotamer: Outliers : 4.56 % Allowed : 20.56 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.25), residues: 1060 helix: -2.67 (0.49), residues: 69 sheet: 0.17 (0.25), residues: 440 loop : -1.67 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 72 TYR 0.026 0.002 TYR D 160 PHE 0.015 0.002 PHE A 143 TRP 0.016 0.002 TRP D 53 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 ( 8322) covalent geometry : angle 0.65536 / 0.33 (11349) SS BOND : bond 0.00545 / 0.34 ( 12) SS BOND : angle 1.25511 / 0.72 ( 24) hydrogen bonds : bond 0.03523 / 2.41 ( 290) hydrogen bonds : angle 5.62870 / 3.98 ( 870) link_BETA1-4 : bond 0.00550 / 0.27 ( 2) link_BETA1-4 : angle 1.37269 / 0.78 ( 6) link_NAG-ASN : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : angle 1.90033 / 1.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 84 time to evaluate : 0.282 Fit side-chains REVERT: A 16 GLN cc_start: 0.7912 (mm110) cc_final: 0.7409 (mp10) REVERT: A 188 GLN cc_start: 0.7678 (mm-40) cc_final: 0.6703 (tp-100) REVERT: E 335 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.5159 (tt) REVERT: E 445 VAL cc_start: 0.8838 (t) cc_final: 0.8548 (m) REVERT: E 458 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8522 (mttp) REVERT: C 83 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7589 (tm-30) REVERT: C 93 TYR cc_start: 0.9060 (t80) cc_final: 0.8692 (t80) REVERT: D 43 LYS cc_start: 0.7666 (mmmm) cc_final: 0.7237 (mmtm) REVERT: D 65 LYS cc_start: 0.8728 (tptt) cc_final: 0.8520 (tttm) REVERT: D 76 LYS cc_start: 0.7970 (mptt) cc_final: 0.7602 (mmtp) outliers start: 41 outliers final: 36 residues processed: 116 average time/residue: 0.0673 time to fit residues: 11.3418 Evaluate side-chains 117 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 80 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108091 restraints weight = 11293.427| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.65 r_work: 0.3204 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8337 Z= 0.173 Angle : 0.614 12.576 11382 Z= 0.309 Chirality : 0.046 0.226 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.796 46.424 1153 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.04 % Favored : 93.87 % Rotamer: Outliers : 4.22 % Allowed : 21.33 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.35 (0.25), residues: 1060 helix: -2.65 (0.50), residues: 69 sheet: 0.19 (0.25), residues: 440 loop : -1.60 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.028 0.002 TYR D 160 PHE 0.022 0.002 PHE A 143 TRP 0.015 0.001 TRP B 50 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 8322) covalent geometry : angle 0.61190 / 0.31 (11349) SS BOND : bond 0.00428 / 0.26 ( 12) SS BOND : angle 1.02107 / 0.58 ( 24) hydrogen bonds : bond 0.03165 / 2.15 ( 290) hydrogen bonds : angle 5.48891 / 3.89 ( 870) link_BETA1-4 : bond 0.00523 / 0.25 ( 2) link_BETA1-4 : angle 1.36914 / 0.77 ( 6) link_NAG-ASN : bond 0.00108 / 0.06 ( 1) link_NAG-ASN : angle 1.85694 / 1.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 0.214 Fit side-chains REVERT: A 16 GLN cc_start: 0.7866 (mm110) cc_final: 0.7366 (mp10) REVERT: A 188 GLN cc_start: 0.7685 (mm-40) cc_final: 0.6727 (tp-100) REVERT: E 335 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.5076 (tt) REVERT: E 445 VAL cc_start: 0.8827 (t) cc_final: 0.8536 (m) REVERT: E 458 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8525 (mttp) REVERT: C 83 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7593 (tm-30) REVERT: C 93 TYR cc_start: 0.9037 (t80) cc_final: 0.8643 (t80) REVERT: D 43 LYS cc_start: 0.7643 (mmmm) cc_final: 0.7204 (mmtm) REVERT: D 65 LYS cc_start: 0.8649 (tptt) cc_final: 0.8434 (tttm) REVERT: D 76 LYS cc_start: 0.7914 (mptt) cc_final: 0.7568 (mmtp) outliers start: 38 outliers final: 35 residues processed: 111 average time/residue: 0.0651 time to fit residues: 10.5254 Evaluate side-chains 116 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 18 optimal weight: 0.0980 chunk 22 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 0.0670 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.161779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114894 restraints weight = 11140.020| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.64 r_work: 0.3281 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8337 Z= 0.090 Angle : 0.559 11.957 11382 Z= 0.278 Chirality : 0.044 0.202 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.297 43.462 1153 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.22 % Allowed : 23.11 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.25), residues: 1060 helix: -2.47 (0.49), residues: 75 sheet: 0.45 (0.25), residues: 443 loop : -1.30 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.030 0.001 TYR D 160 PHE 0.031 0.001 PHE A 143 TRP 0.016 0.001 TRP B 50 HIS 0.004 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 ( 8322) covalent geometry : angle 0.55712 / 0.28 (11349) SS BOND : bond 0.00374 / 0.24 ( 12) SS BOND : angle 0.76257 / 0.43 ( 24) hydrogen bonds : bond 0.02582 / 1.71 ( 290) hydrogen bonds : angle 5.05542 / 3.59 ( 870) link_BETA1-4 : bond 0.00524 / 0.26 ( 2) link_BETA1-4 : angle 1.43382 / 0.79 ( 6) link_NAG-ASN : bond 0.00155 / 0.08 ( 1) link_NAG-ASN : angle 1.55418 / 0.97 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.294 Fit side-chains REVERT: A 16 GLN cc_start: 0.7823 (mm110) cc_final: 0.7378 (mp10) REVERT: A 188 GLN cc_start: 0.7683 (mm-40) cc_final: 0.6794 (tp-100) REVERT: B 105 ASN cc_start: 0.8991 (m-40) cc_final: 0.8787 (t0) REVERT: E 335 LEU cc_start: 0.5128 (OUTLIER) cc_final: 0.4882 (tt) REVERT: E 458 LYS cc_start: 0.9037 (mtmt) cc_final: 0.8392 (mttp) REVERT: C 83 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7557 (tm-30) REVERT: C 93 TYR cc_start: 0.8889 (t80) cc_final: 0.8554 (t80) REVERT: D 43 LYS cc_start: 0.7750 (mmmm) cc_final: 0.7420 (mmtm) REVERT: D 65 LYS cc_start: 0.8310 (tptt) cc_final: 0.8065 (tttm) outliers start: 20 outliers final: 17 residues processed: 102 average time/residue: 0.0700 time to fit residues: 10.6539 Evaluate side-chains 99 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.157961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110761 restraints weight = 11257.930| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.63 r_work: 0.3233 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8337 Z= 0.155 Angle : 0.589 12.412 11382 Z= 0.296 Chirality : 0.045 0.210 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.475 43.037 1153 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.06 % Rotamer: Outliers : 2.56 % Allowed : 22.89 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.02 (0.25), residues: 1060 helix: -2.50 (0.49), residues: 75 sheet: 0.40 (0.25), residues: 446 loop : -1.35 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.027 0.001 TYR D 160 PHE 0.012 0.002 PHE E 392 TRP 0.015 0.001 TRP B 50 HIS 0.004 0.001 HIS D 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 8322) covalent geometry : angle 0.58695 / 0.30 (11349) SS BOND : bond 0.00417 / 0.25 ( 12) SS BOND : angle 0.91047 / 0.52 ( 24) hydrogen bonds : bond 0.02955 / 1.99 ( 290) hydrogen bonds : angle 5.16386 / 3.66 ( 870) link_BETA1-4 : bond 0.00438 / 0.22 ( 2) link_BETA1-4 : angle 1.30100 / 0.72 ( 6) link_NAG-ASN : bond 0.00208 / 0.11 ( 1) link_NAG-ASN : angle 1.69997 / 1.07 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.59 seconds wall clock time: 39 minutes 49.65 seconds (2389.65 seconds total)