Starting phenix.real_space_refine on Wed Mar 12 19:20:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m42_23662/03_2025/7m42_23662.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m42_23662/03_2025/7m42_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m42_23662/03_2025/7m42_23662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m42_23662/03_2025/7m42_23662.map" model { file = "/net/cci-nas-00/data/ceres_data/7m42_23662/03_2025/7m42_23662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m42_23662/03_2025/7m42_23662.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.22, per 1000 atoms: 0.64 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: 2.07 Conformation dependent library (CDL) restraints added in 952.7 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: 1.17 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: 2.63 Time building geometry restraints manager: 2.44 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 - 21.96: 4677 21.96 - 43.91: 243 43.91 - 65.87: 33 65.87 - 87.82: 17 87.82 - 109.78: 4 Dihedral angle restraints: 4974 sinusoidal: 1901 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 4971 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.210 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 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 8322 Z= 0.130 Angle : 0.557 9.147 11349 Z= 0.296 Chirality : 0.045 0.258 1271 Planarity : 0.004 0.042 1456 Dihedral : 13.897 109.779 2984 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.001 TRP B 50 HIS 0.001 0.000 HIS B 210 PHE 0.008 0.001 PHE C 145 TYR 0.019 0.001 TYR E 351 ARG 0.007 0.000 ARG E 355 *********************** 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 : 0.908 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: 0.8099 (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: 0.1958 time to fit residues: 38.0919 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 : 0.974 ------------------------------------------------------------------------------- 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 88 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 82 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 198 GLN E 370 ASN C 16 GLN C 28 ASN C 194 HIS D 170 ASN D 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.168976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120767 restraints weight = 11247.120| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.71 r_work: 0.3368 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8322 Z= 0.134 Angle : 0.531 11.212 11349 Z= 0.268 Chirality : 0.044 0.175 1271 Planarity : 0.004 0.042 1456 Dihedral : 6.263 63.617 1216 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 3.00 % Allowed : 14.11 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.24), residues: 1060 helix: -3.04 (0.44), residues: 74 sheet: -0.18 (0.24), residues: 441 loop : -1.87 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 53 HIS 0.002 0.000 HIS D 35 PHE 0.009 0.001 PHE E 377 TYR 0.025 0.001 TYR C 93 ARG 0.003 0.000 ARG D 16 *********************** 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 121 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.876 Fit side-chains REVERT: E 335 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.5125 (tt) REVERT: E 354 ASN cc_start: 0.8694 (t0) cc_final: 0.8469 (t0) REVERT: E 458 LYS cc_start: 0.9006 (mtmt) cc_final: 0.8487 (mttp) REVERT: C 83 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7614 (tm-30) REVERT: C 190 GLN cc_start: 0.5830 (mt0) cc_final: 0.5343 (mp10) outliers start: 27 outliers final: 18 residues processed: 115 average time/residue: 0.1742 time to fit residues: 29.4349 Evaluate side-chains 106 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 119 VAL 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 35 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 69 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 41 HIS A 192 HIS E 394 ASN E 493 GLN C 28 ASN ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.152628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107600 restraints weight = 11438.281| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.02 r_work: 0.3140 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 8322 Z= 0.600 Angle : 0.782 10.275 11349 Z= 0.408 Chirality : 0.051 0.205 1271 Planarity : 0.006 0.047 1456 Dihedral : 6.216 47.458 1214 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.92 % Favored : 91.98 % Rotamer: Outliers : 5.33 % Allowed : 17.56 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.24), residues: 1060 helix: -2.77 (0.47), residues: 67 sheet: -0.20 (0.25), residues: 431 loop : -2.09 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 53 HIS 0.006 0.002 HIS D 35 PHE 0.021 0.003 PHE D 27 TYR 0.026 0.003 TYR C 101 ARG 0.007 0.001 ARG D 72 *********************** 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 144 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7134 (mm-40) REVERT: E 335 LEU cc_start: 0.5460 (OUTLIER) cc_final: 0.5100 (tt) REVERT: E 458 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8510 (mttp) REVERT: C 62 ASP cc_start: 0.8158 (t0) cc_final: 0.7889 (t0) REVERT: C 83 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7609 (tm-30) REVERT: C 93 TYR cc_start: 0.9092 (t80) cc_final: 0.8703 (t80) REVERT: C 97 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8882 (pp) REVERT: D 43 LYS cc_start: 0.7834 (mmmm) cc_final: 0.7302 (mmtm) REVERT: D 76 LYS cc_start: 0.8076 (mptt) cc_final: 0.7676 (mmtp) outliers start: 48 outliers final: 37 residues processed: 129 average time/residue: 0.2022 time to fit residues: 36.7615 Evaluate side-chains 124 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 148 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 76 ILE 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 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 471 GLU 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 C residue 19 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 97 LEU 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 99 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 20 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 1 optimal weight: 0.0270 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.159598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112346 restraints weight = 11081.548| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.63 r_work: 0.3251 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8322 Z= 0.148 Angle : 0.567 11.181 11349 Z= 0.286 Chirality : 0.044 0.182 1271 Planarity : 0.004 0.047 1456 Dihedral : 4.904 49.904 1214 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 3.00 % Allowed : 21.78 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.25), residues: 1060 helix: -2.53 (0.50), residues: 67 sheet: -0.01 (0.24), residues: 447 loop : -1.72 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 50 HIS 0.002 0.001 HIS D 35 PHE 0.010 0.001 PHE C 145 TYR 0.026 0.001 TYR C 51 ARG 0.003 0.000 ARG D 72 *********************** 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 119 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7283 (mp10) cc_final: 0.6734 (mp10) REVERT: A 56 ARG cc_start: 0.8481 (ptt-90) cc_final: 0.8134 (ptp90) REVERT: A 188 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7259 (mm-40) REVERT: E 335 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.5012 (tt) REVERT: E 458 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8489 (mttp) REVERT: C 83 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7533 (tm-30) REVERT: C 93 TYR cc_start: 0.8988 (t80) cc_final: 0.8654 (t80) REVERT: D 43 LYS cc_start: 0.7670 (mmmm) cc_final: 0.7293 (mmtm) outliers start: 27 outliers final: 18 residues processed: 110 average time/residue: 0.1661 time to fit residues: 26.3205 Evaluate side-chains 103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL 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 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 134 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 478 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 46 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.156741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108437 restraints weight = 11261.817| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.65 r_work: 0.3194 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8322 Z= 0.305 Angle : 0.618 9.542 11349 Z= 0.314 Chirality : 0.046 0.213 1271 Planarity : 0.005 0.046 1456 Dihedral : 5.094 48.004 1214 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.42 % Favored : 93.49 % Rotamer: Outliers : 4.67 % Allowed : 20.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1060 helix: -2.49 (0.51), residues: 67 sheet: 0.08 (0.25), residues: 446 loop : -1.71 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 50 HIS 0.006 0.001 HIS D 215 PHE 0.014 0.002 PHE B 176 TYR 0.025 0.002 TYR D 160 ARG 0.004 0.000 ARG D 72 *********************** 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 129 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 87 time to evaluate : 0.878 Fit side-chains REVERT: A 16 GLN cc_start: 0.7548 (mp10) cc_final: 0.6942 (mp10) REVERT: A 188 GLN cc_start: 0.7695 (mm-40) cc_final: 0.6686 (tp-100) REVERT: E 335 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.5069 (tt) REVERT: E 420 ASP cc_start: 0.8461 (m-30) cc_final: 0.8010 (m-30) REVERT: E 458 LYS cc_start: 0.9040 (mtmt) cc_final: 0.8516 (mttp) REVERT: C 83 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7590 (tm-30) REVERT: C 93 TYR cc_start: 0.9071 (t80) cc_final: 0.8663 (t80) REVERT: D 43 LYS cc_start: 0.7687 (mmmm) cc_final: 0.7254 (mmtm) REVERT: D 76 LYS cc_start: 0.7967 (mptt) cc_final: 0.7592 (mmtp) outliers start: 42 outliers final: 32 residues processed: 115 average time/residue: 0.1797 time to fit residues: 29.9701 Evaluate side-chains 118 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 148 VAL 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 503 VAL Chi-restraints excluded: chain E residue 524 VAL 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 65 LYS Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 35 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.157272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.109929 restraints weight = 11082.830| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.63 r_work: 0.3208 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8322 Z= 0.243 Angle : 0.591 11.086 11349 Z= 0.298 Chirality : 0.045 0.198 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.985 47.089 1214 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.62 % Rotamer: Outliers : 4.00 % Allowed : 21.22 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.25), residues: 1060 helix: -2.34 (0.55), residues: 61 sheet: 0.15 (0.25), residues: 446 loop : -1.65 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 50 HIS 0.004 0.001 HIS D 215 PHE 0.010 0.001 PHE C 145 TYR 0.027 0.001 TYR D 160 ARG 0.004 0.000 ARG D 72 *********************** 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 123 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.887 Fit side-chains REVERT: A 16 GLN cc_start: 0.7451 (mp10) cc_final: 0.6808 (mp10) REVERT: A 188 GLN cc_start: 0.7660 (mm-40) cc_final: 0.6653 (tp-100) REVERT: E 335 LEU cc_start: 0.5406 (OUTLIER) cc_final: 0.5084 (tt) REVERT: E 420 ASP cc_start: 0.8449 (m-30) cc_final: 0.8046 (m-30) REVERT: E 458 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8514 (mttp) REVERT: C 83 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7583 (tm-30) REVERT: C 93 TYR cc_start: 0.9046 (t80) cc_final: 0.8633 (t80) REVERT: D 43 LYS cc_start: 0.7652 (mmmm) cc_final: 0.7215 (mmtm) REVERT: D 76 LYS cc_start: 0.7930 (mptt) cc_final: 0.7557 (mmtp) outliers start: 36 outliers final: 31 residues processed: 113 average time/residue: 0.1689 time to fit residues: 27.6815 Evaluate side-chains 116 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 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 503 VAL Chi-restraints excluded: chain E residue 524 VAL 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 22 CYS Chi-restraints excluded: chain D residue 70 ILE 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 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 58 optimal weight: 0.0010 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.160820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112524 restraints weight = 11306.445| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.68 r_work: 0.3260 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8322 Z= 0.152 Angle : 0.554 10.594 11349 Z= 0.277 Chirality : 0.044 0.199 1271 Planarity : 0.004 0.045 1456 Dihedral : 4.632 44.766 1214 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.33 % Allowed : 22.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.25), residues: 1060 helix: -2.20 (0.57), residues: 61 sheet: 0.25 (0.25), residues: 447 loop : -1.45 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 50 HIS 0.003 0.001 HIS D 35 PHE 0.009 0.001 PHE C 145 TYR 0.030 0.001 TYR D 160 ARG 0.002 0.000 ARG D 72 *********************** 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 114 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.902 Fit side-chains REVERT: A 16 GLN cc_start: 0.7500 (mp10) cc_final: 0.6851 (mp10) REVERT: A 188 GLN cc_start: 0.7637 (mm-40) cc_final: 0.6740 (tp-100) REVERT: E 335 LEU cc_start: 0.5297 (OUTLIER) cc_final: 0.5015 (tt) REVERT: E 420 ASP cc_start: 0.8418 (m-30) cc_final: 0.8032 (m-30) REVERT: E 458 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8400 (mttp) REVERT: C 83 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7593 (tm-30) REVERT: C 93 TYR cc_start: 0.8990 (t80) cc_final: 0.8614 (t80) REVERT: D 43 LYS cc_start: 0.7628 (mmmm) cc_final: 0.7270 (mmtm) outliers start: 30 outliers final: 24 residues processed: 107 average time/residue: 0.1621 time to fit residues: 25.6700 Evaluate side-chains 108 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.159707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112262 restraints weight = 11213.091| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.64 r_work: 0.3244 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8322 Z= 0.157 Angle : 0.554 11.286 11349 Z= 0.276 Chirality : 0.044 0.192 1271 Planarity : 0.004 0.045 1456 Dihedral : 4.578 43.377 1214 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.89 % Allowed : 22.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.25), residues: 1060 helix: -2.11 (0.57), residues: 61 sheet: 0.35 (0.25), residues: 447 loop : -1.35 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 50 HIS 0.003 0.001 HIS D 215 PHE 0.008 0.001 PHE C 145 TYR 0.028 0.001 TYR D 160 ARG 0.002 0.000 ARG D 72 *********************** 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 112 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.950 Fit side-chains REVERT: A 16 GLN cc_start: 0.7440 (mp10) cc_final: 0.6757 (mp10) REVERT: A 188 GLN cc_start: 0.7621 (mm-40) cc_final: 0.6717 (tp-100) REVERT: E 335 LEU cc_start: 0.5235 (OUTLIER) cc_final: 0.4962 (tt) REVERT: E 420 ASP cc_start: 0.8409 (m-30) cc_final: 0.8005 (m-30) REVERT: E 458 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8430 (mttp) REVERT: C 83 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7584 (tm-30) REVERT: C 93 TYR cc_start: 0.8963 (t80) cc_final: 0.8577 (t80) REVERT: D 43 LYS cc_start: 0.7773 (mmmm) cc_final: 0.7406 (mmtm) REVERT: D 216 LYS cc_start: 0.5250 (OUTLIER) cc_final: 0.5037 (ptmm) outliers start: 26 outliers final: 22 residues processed: 107 average time/residue: 0.1853 time to fit residues: 30.1231 Evaluate side-chains 107 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 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 468 ILE Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 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 70 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 216 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 80 optimal weight: 7.9990 chunk 25 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111468 restraints weight = 11262.007| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.62 r_work: 0.3224 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8322 Z= 0.211 Angle : 0.572 11.971 11349 Z= 0.287 Chirality : 0.045 0.206 1271 Planarity : 0.004 0.045 1456 Dihedral : 4.712 43.503 1214 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.00 % Allowed : 22.67 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1060 helix: -2.06 (0.57), residues: 61 sheet: 0.38 (0.25), residues: 447 loop : -1.37 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 50 HIS 0.003 0.001 HIS D 215 PHE 0.010 0.001 PHE E 377 TYR 0.028 0.001 TYR C 51 ARG 0.003 0.000 ARG E 457 *********************** 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 112 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.935 Fit side-chains REVERT: A 188 GLN cc_start: 0.7593 (mm-40) cc_final: 0.6715 (tp-100) REVERT: E 335 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.4993 (tt) REVERT: E 420 ASP cc_start: 0.8429 (m-30) cc_final: 0.8026 (m-30) REVERT: E 458 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8450 (mttp) REVERT: C 16 GLN cc_start: 0.8517 (tt0) cc_final: 0.8307 (pt0) REVERT: C 83 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7616 (tm-30) REVERT: C 93 TYR cc_start: 0.8968 (t80) cc_final: 0.8598 (t80) REVERT: D 43 LYS cc_start: 0.7806 (mmmm) cc_final: 0.7384 (mmtm) REVERT: D 76 LYS cc_start: 0.7874 (mptt) cc_final: 0.7506 (mmtp) outliers start: 27 outliers final: 24 residues processed: 106 average time/residue: 0.1682 time to fit residues: 25.9798 Evaluate side-chains 109 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 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 122 SER 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 468 ILE 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 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 91 THR 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 59 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 40.0000 chunk 95 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 98 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.159641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112371 restraints weight = 11186.206| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.63 r_work: 0.3251 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8322 Z= 0.181 Angle : 0.561 12.059 11349 Z= 0.281 Chirality : 0.044 0.200 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.637 43.223 1214 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.89 % Allowed : 22.78 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.25), residues: 1060 helix: -2.00 (0.58), residues: 61 sheet: 0.44 (0.25), residues: 447 loop : -1.33 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 50 HIS 0.003 0.001 HIS D 35 PHE 0.009 0.001 PHE C 145 TYR 0.029 0.001 TYR C 51 ARG 0.002 0.000 ARG D 72 ********************** 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 112 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.976 Fit side-chains REVERT: A 188 GLN cc_start: 0.7599 (mm-40) cc_final: 0.6734 (tp-100) REVERT: E 335 LEU cc_start: 0.5252 (OUTLIER) cc_final: 0.4979 (tt) REVERT: E 420 ASP cc_start: 0.8416 (m-30) cc_final: 0.8014 (m-30) REVERT: E 458 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8468 (mttp) REVERT: C 16 GLN cc_start: 0.8514 (tt0) cc_final: 0.8294 (pt0) REVERT: C 83 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 93 TYR cc_start: 0.8964 (t80) cc_final: 0.8613 (t80) REVERT: D 43 LYS cc_start: 0.7836 (mmmm) cc_final: 0.7430 (mmtm) outliers start: 26 outliers final: 25 residues processed: 106 average time/residue: 0.1661 time to fit residues: 25.7481 Evaluate side-chains 112 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 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 122 SER 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 468 ILE 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 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 216 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110986 restraints weight = 11370.676| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.69 r_work: 0.3241 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8322 Z= 0.210 Angle : 0.576 13.037 11349 Z= 0.289 Chirality : 0.045 0.203 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.720 43.223 1214 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.33 % Allowed : 22.44 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1060 helix: -1.98 (0.58), residues: 61 sheet: 0.47 (0.25), residues: 446 loop : -1.37 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 50 HIS 0.003 0.001 HIS D 215 PHE 0.012 0.001 PHE E 392 TYR 0.029 0.001 TYR C 51 ARG 0.003 0.000 ARG D 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5595.45 seconds wall clock time: 98 minutes 25.20 seconds (5905.20 seconds total)