Starting phenix.real_space_refine on Tue Aug 4 17:53:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t5j_55585/08_2026/9t5j_55585.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t5j_55585/08_2026/9t5j_55585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t5j_55585/08_2026/9t5j_55585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t5j_55585/08_2026/9t5j_55585.map" model { file = "/net/cci-nas-00/data/ceres_data/9t5j_55585/08_2026/9t5j_55585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t5j_55585/08_2026/9t5j_55585.cif" } resolution = 2.8 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= 0.001 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 3548 2.51 5 N 901 2.21 5 O 1037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5525 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1556 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain breaks: 2 Chain: "B" Number of atoms: 1991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1991 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1920 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.41, per 1000 atoms: 0.26 Number of scatterers: 5525 At special positions: 0 Unit cell: (67.3344, 87.3744, 96.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 4 15.00 Mg 2 11.99 O 1037 8.00 N 901 7.00 C 3548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 141.8 milliseconds 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 2 sheets defined 66.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 359 through 378 Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.818A pdb=" N THR A 441 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 460 removed outlier: 3.618A pdb=" N GLU A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 458 " --> pdb=" O LYS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 3.621A pdb=" N ASN A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 519 removed outlier: 3.918A pdb=" N LEU A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 537 removed outlier: 4.917A pdb=" N THR A 530 " --> pdb=" O GLY A 526 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLN A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 569 Proline residue: A 566 - end of helix Processing helix chain 'A' and resid 574 through 591 Processing helix chain 'A' and resid 594 through 604 removed outlier: 3.928A pdb=" N SER A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 46 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.741A pdb=" N LYS B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 removed outlier: 3.750A pdb=" N ARG B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.926A pdb=" N VAL B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 removed outlier: 4.333A pdb=" N PHE B 130 " --> pdb=" O GLN B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 Processing helix chain 'B' and resid 162 through 181 Processing helix chain 'B' and resid 196 through 205 Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 221 through 235 removed outlier: 3.796A pdb=" N GLU B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 250 through 269 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 54 through 59 Processing helix chain 'C' and resid 74 through 87 removed outlier: 4.455A pdb=" N VAL C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 97 through 100 Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 118 through 130 removed outlier: 3.962A pdb=" N GLN C 122 " --> pdb=" O PRO C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 removed outlier: 4.116A pdb=" N VAL C 146 " --> pdb=" O GLN C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 146' Processing helix chain 'C' and resid 147 through 165 removed outlier: 4.130A pdb=" N SER C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 180 through 191 removed outlier: 3.717A pdb=" N LYS C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 207 through 225 removed outlier: 3.584A pdb=" N LYS C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 237 through 253 Processing sheet with id=AA1, first strand: chain 'B' and resid 68 through 69 removed outlier: 6.135A pdb=" N CYS B 21 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 152 " --> pdb=" O CYS B 21 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 23 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL B 154 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU B 25 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N ASP B 156 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG B 239 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 50 through 53 removed outlier: 7.051A pdb=" N VAL C 36 " --> pdb=" O MET C 51 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP C 53 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN C 38 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN C 35 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASP C 106 " --> pdb=" O GLN C 35 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL C 37 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR C 4 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE C 105 " --> pdb=" O TYR C 4 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN C 6 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL C 170 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY C 136 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE C 172 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE C 138 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C 174 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 140 " --> pdb=" O THR C 174 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 0.52 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: 1742 1.34 - 1.46: 778 1.46 - 1.57: 3054 1.57 - 1.69: 6 1.69 - 1.81: 57 Bond restraints: 5637 Sorted by residual: bond pdb=" CG1 ILE B 176 " pdb=" CD1 ILE B 176 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.65e+00 bond pdb=" C5 GDP B 401 " pdb=" C4 GDP B 401 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.54e+00 bond pdb=" C5 GDP C 301 " pdb=" C4 GDP C 301 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" CB VAL B 62 " pdb=" CG1 VAL B 62 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CB ILE C 172 " pdb=" CG2 ILE C 172 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.94e-01 ... (remaining 5632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 7489 2.13 - 4.26: 138 4.26 - 6.39: 10 6.39 - 8.51: 2 8.51 - 10.64: 2 Bond angle restraints: 7641 Sorted by residual: angle pdb=" C3' GDP C 301 " pdb=" C2' GDP C 301 " pdb=" C1' GDP C 301 " ideal model delta sigma weight residual 111.00 100.36 10.64 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C3' GDP B 401 " pdb=" C2' GDP B 401 " pdb=" C1' GDP B 401 " ideal model delta sigma weight residual 111.00 101.57 9.43 3.00e+00 1.11e-01 9.88e+00 angle pdb=" C4' GDP C 301 " pdb=" C3' GDP C 301 " pdb=" C2' GDP C 301 " ideal model delta sigma weight residual 111.00 103.06 7.94 3.00e+00 1.11e-01 7.01e+00 angle pdb=" N PRO C 118 " pdb=" CA PRO C 118 " pdb=" C PRO C 118 " ideal model delta sigma weight residual 112.47 117.76 -5.29 2.06e+00 2.36e-01 6.60e+00 angle pdb=" C4' GDP B 401 " pdb=" C3' GDP B 401 " pdb=" C2' GDP B 401 " ideal model delta sigma weight residual 111.00 103.91 7.09 3.00e+00 1.11e-01 5.59e+00 ... (remaining 7636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.69: 3299 29.69 - 59.39: 82 59.39 - 89.08: 9 89.08 - 118.77: 2 118.77 - 148.46: 2 Dihedral angle restraints: 3394 sinusoidal: 1392 harmonic: 2002 Sorted by residual: dihedral pdb=" O2B GDP B 401 " pdb=" O3A GDP B 401 " pdb=" PB GDP B 401 " pdb=" PA GDP B 401 " ideal model delta sinusoidal sigma weight residual -180.00 -31.54 -148.46 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" O2B GDP C 301 " pdb=" O3A GDP C 301 " pdb=" PB GDP C 301 " pdb=" PA GDP C 301 " ideal model delta sinusoidal sigma weight residual -180.00 -37.21 -142.79 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" C5' GDP C 301 " pdb=" O5' GDP C 301 " pdb=" PA GDP C 301 " pdb=" O3A GDP C 301 " ideal model delta sinusoidal sigma weight residual 179.98 -67.94 -112.08 1 2.00e+01 2.50e-03 3.30e+01 ... (remaining 3391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 525 0.041 - 0.082: 281 0.082 - 0.123: 55 0.123 - 0.163: 17 0.163 - 0.204: 3 Chirality restraints: 881 Sorted by residual: chirality pdb=" CB ILE C 172 " pdb=" CA ILE C 172 " pdb=" CG1 ILE C 172 " pdb=" CG2 ILE C 172 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA LYS B 190 " pdb=" N LYS B 190 " pdb=" C LYS B 190 " pdb=" CB LYS B 190 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" C3' GDP C 301 " pdb=" C4' GDP C 301 " pdb=" O3' GDP C 301 " pdb=" C2' GDP C 301 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 878 not shown) Planarity restraints: 952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 269 " 0.001 2.00e-02 2.50e+03 1.86e-02 6.89e+00 pdb=" CG TYR B 269 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR B 269 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 269 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 269 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B 269 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 269 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR B 269 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 71 " -0.196 9.50e-02 1.11e+02 8.87e-02 6.57e+00 pdb=" NE ARG B 71 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 71 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG B 71 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 71 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 172 " 0.015 2.00e-02 2.50e+03 1.77e-02 6.24e+00 pdb=" CG TYR B 172 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 172 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 172 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 172 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B 172 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 172 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR B 172 " 0.023 2.00e-02 2.50e+03 ... (remaining 949 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 4 2.19 - 2.87: 1949 2.87 - 3.54: 7966 3.54 - 4.22: 13854 4.22 - 4.90: 23705 Nonbonded interactions: 47478 Sorted by model distance: nonbonded pdb=" O2B GDP C 301 " pdb="MG MG C 302 " model vdw 1.512 2.170 nonbonded pdb=" OG1 THR B 33 " pdb="MG MG B 402 " model vdw 2.048 2.170 nonbonded pdb=" O2B GDP B 401 " pdb="MG MG B 402 " model vdw 2.116 2.170 nonbonded pdb=" OG SER C 17 " pdb="MG MG C 302 " model vdw 2.161 2.170 nonbonded pdb=" OG SER C 17 " pdb=" O2B GDP C 301 " model vdw 2.267 3.040 ... (remaining 47473 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: 1.840 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.860 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.005 0.050 5637 Z= 0.198 Angle : 0.742 10.643 7641 Z= 0.403 Chirality : 0.050 0.204 881 Planarity : 0.008 0.089 952 Dihedral : 14.383 148.464 2094 Min Nonbonded Distance : 1.512 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.32 % Allowed : 2.27 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.80 (0.29), residues: 670 helix: -1.37 (0.21), residues: 398 sheet: -0.60 (0.65), residues: 68 loop : -0.53 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.004 ARG B 71 TYR 0.027 0.006 TYR B 269 PHE 0.022 0.002 PHE B 184 TRP 0.018 0.002 TRP C 130 HIS 0.007 0.002 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 ( 5637) covalent geometry : angle 0.74234 / 0.40 ( 7641) hydrogen bonds : bond 0.16031 / 11.32 ( 307) hydrogen bonds : angle 7.29168 / 5.12 ( 903) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7074 (tt0) REVERT: A 508 GLU cc_start: 0.8002 (tt0) cc_final: 0.7653 (tm-30) REVERT: B 77 LYS cc_start: 0.8908 (mttt) cc_final: 0.8673 (mttp) REVERT: B 110 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6786 (mp0) REVERT: B 170 MET cc_start: 0.8394 (mmt) cc_final: 0.7939 (mmm) REVERT: B 181 LYS cc_start: 0.8287 (tttt) cc_final: 0.7478 (tttp) REVERT: B 270 ARG cc_start: 0.6305 (ttt180) cc_final: 0.5452 (ttm170) REVERT: C 59 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7226 (mp0) REVERT: C 82 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7773 (mt-10) REVERT: C 115 THR cc_start: 0.8607 (t) cc_final: 0.8123 (p) REVERT: C 150 LYS cc_start: 0.8462 (mttt) cc_final: 0.8218 (mtpt) REVERT: C 195 MET cc_start: 0.8071 (mmm) cc_final: 0.7869 (mpp) outliers start: 2 outliers final: 0 residues processed: 205 average time/residue: 0.6856 time to fit residues: 145.5570 Evaluate side-chains 121 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 GLN A 500 GLN A 534 ASN A 543 ASN B 37 GLN B 44 HIS B 169 ASN B 189 ASN B 222 ASN C 38 ASN C 74 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.133525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.110630 restraints weight = 8289.381| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.44 r_work: 0.3411 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5637 Z= 0.161 Angle : 0.654 7.371 7641 Z= 0.330 Chirality : 0.044 0.183 881 Planarity : 0.004 0.040 952 Dihedral : 9.675 138.029 750 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.38 % Allowed : 13.31 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.31), residues: 670 helix: 0.28 (0.24), residues: 406 sheet: 0.15 (0.69), residues: 55 loop : -0.24 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 225 TYR 0.012 0.002 TYR A 449 PHE 0.028 0.002 PHE A 583 TRP 0.008 0.001 TRP B 132 HIS 0.003 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 5637) covalent geometry : angle 0.65436 / 0.33 ( 7641) hydrogen bonds : bond 0.04602 / 3.17 ( 307) hydrogen bonds : angle 5.24139 / 3.62 ( 903) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.220 Fit side-chains REVERT: A 534 ASN cc_start: 0.8757 (m-40) cc_final: 0.8554 (m110) REVERT: A 589 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 595 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7777 (t0) REVERT: B 43 LEU cc_start: 0.8636 (mt) cc_final: 0.8426 (mt) REVERT: B 107 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7491 (mmpt) REVERT: B 181 LYS cc_start: 0.8106 (tttt) cc_final: 0.7893 (mtpp) REVERT: B 265 TYR cc_start: 0.7332 (t80) cc_final: 0.6844 (t80) REVERT: B 269 TYR cc_start: 0.5687 (m-80) cc_final: 0.5404 (m-10) REVERT: C 82 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7541 (mt-10) REVERT: C 195 MET cc_start: 0.8069 (mmm) cc_final: 0.7722 (mpp) REVERT: C 207 ARG cc_start: 0.6398 (pmt-80) cc_final: 0.5963 (mpp-170) outliers start: 27 outliers final: 5 residues processed: 161 average time/residue: 0.5594 time to fit residues: 94.1495 Evaluate side-chains 118 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 163 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 20 optimal weight: 0.0570 chunk 57 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.0040 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.4510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN A 543 ASN A 592 HIS B 88 ASN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.134671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.112331 restraints weight = 8237.426| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.48 r_work: 0.3427 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5637 Z= 0.139 Angle : 0.603 7.427 7641 Z= 0.300 Chirality : 0.043 0.164 881 Planarity : 0.004 0.039 952 Dihedral : 8.670 125.746 750 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.06 % Allowed : 16.72 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.33), residues: 670 helix: 0.75 (0.25), residues: 408 sheet: -0.25 (0.67), residues: 59 loop : 0.09 (0.47), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 229 TYR 0.019 0.002 TYR B 51 PHE 0.023 0.002 PHE C 88 TRP 0.007 0.001 TRP C 130 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 5637) covalent geometry : angle 0.60280 / 0.30 ( 7641) hydrogen bonds : bond 0.03985 / 2.74 ( 307) hydrogen bonds : angle 5.00298 / 3.45 ( 903) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 565 THR cc_start: 0.6027 (OUTLIER) cc_final: 0.5810 (p) REVERT: A 589 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7285 (mm-30) REVERT: A 595 ASN cc_start: 0.8119 (t0) cc_final: 0.7895 (t0) REVERT: B 43 LEU cc_start: 0.8470 (mt) cc_final: 0.8193 (mp) REVERT: B 107 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7425 (mmpt) REVERT: B 225 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7497 (ttp-110) REVERT: B 265 TYR cc_start: 0.7407 (t80) cc_final: 0.7047 (t80) REVERT: C 79 PHE cc_start: 0.7901 (t80) cc_final: 0.7686 (t80) REVERT: C 82 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7440 (mt-10) REVERT: C 145 MET cc_start: 0.8141 (mmm) cc_final: 0.7544 (mtp) REVERT: C 207 ARG cc_start: 0.6308 (pmt-80) cc_final: 0.5890 (mpp-170) outliers start: 25 outliers final: 5 residues processed: 146 average time/residue: 0.5416 time to fit residues: 82.7511 Evaluate side-chains 114 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 187 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 GLN A 500 GLN A 543 ASN B 88 ASN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.134360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111735 restraints weight = 8193.360| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.47 r_work: 0.3424 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5637 Z= 0.148 Angle : 0.614 7.145 7641 Z= 0.302 Chirality : 0.043 0.159 881 Planarity : 0.004 0.039 952 Dihedral : 8.314 116.783 750 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 4.55 % Allowed : 18.83 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.33), residues: 670 helix: 0.99 (0.25), residues: 404 sheet: -0.29 (0.68), residues: 59 loop : 0.16 (0.47), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 71 TYR 0.016 0.002 TYR B 51 PHE 0.021 0.002 PHE A 583 TRP 0.006 0.001 TRP C 130 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 5637) covalent geometry : angle 0.61377 / 0.30 ( 7641) hydrogen bonds : bond 0.03897 / 2.70 ( 307) hydrogen bonds : angle 4.89479 / 3.36 ( 903) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 459 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7812 (tt) REVERT: A 500 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7258 (mp10) REVERT: A 589 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7252 (mm-30) REVERT: A 595 ASN cc_start: 0.8118 (t0) cc_final: 0.7860 (t0) REVERT: B 43 LEU cc_start: 0.8438 (mt) cc_final: 0.8151 (mp) REVERT: B 107 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7457 (mmpt) REVERT: B 225 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7459 (ttm-80) REVERT: B 265 TYR cc_start: 0.7495 (t80) cc_final: 0.6766 (t80) REVERT: B 266 GLU cc_start: 0.7959 (tp30) cc_final: 0.7694 (tp30) REVERT: C 82 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7411 (mt-10) REVERT: C 145 MET cc_start: 0.8078 (mmm) cc_final: 0.7555 (mtp) REVERT: C 192 ASP cc_start: 0.7700 (t0) cc_final: 0.7442 (t0) REVERT: C 207 ARG cc_start: 0.6448 (pmt-80) cc_final: 0.6036 (mpp-170) outliers start: 28 outliers final: 9 residues processed: 141 average time/residue: 0.4996 time to fit residues: 73.9331 Evaluate side-chains 115 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 223 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 47 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 0.0370 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.135278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112771 restraints weight = 8394.496| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.50 r_work: 0.3446 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5637 Z= 0.140 Angle : 0.616 9.028 7641 Z= 0.299 Chirality : 0.043 0.166 881 Planarity : 0.004 0.039 952 Dihedral : 8.068 110.092 750 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.38 % Allowed : 19.48 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.33), residues: 670 helix: 1.07 (0.25), residues: 404 sheet: -0.56 (0.65), residues: 69 loop : 0.29 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 71 TYR 0.011 0.001 TYR B 76 PHE 0.012 0.002 PHE C 79 TRP 0.010 0.001 TRP C 130 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 5637) covalent geometry : angle 0.61609 / 0.30 ( 7641) hydrogen bonds : bond 0.03763 / 2.59 ( 307) hydrogen bonds : angle 4.82580 / 3.31 ( 903) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7720 (tt) REVERT: A 500 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7242 (mp10) REVERT: A 589 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7182 (mm-30) REVERT: A 595 ASN cc_start: 0.8113 (t0) cc_final: 0.7851 (t0) REVERT: B 51 TYR cc_start: 0.7514 (t80) cc_final: 0.7068 (t80) REVERT: B 107 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7406 (mmpt) REVERT: B 230 VAL cc_start: 0.8301 (p) cc_final: 0.8062 (t) REVERT: B 265 TYR cc_start: 0.7258 (t80) cc_final: 0.6498 (t80) REVERT: B 266 GLU cc_start: 0.7914 (tp30) cc_final: 0.7608 (tp30) REVERT: C 82 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7381 (mt-10) REVERT: C 120 MET cc_start: 0.7830 (mmp) cc_final: 0.7510 (mmm) REVERT: C 145 MET cc_start: 0.8041 (mmm) cc_final: 0.7543 (mtp) REVERT: C 192 ASP cc_start: 0.7692 (t0) cc_final: 0.7403 (t0) REVERT: C 207 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.6109 (mpp-170) outliers start: 27 outliers final: 14 residues processed: 134 average time/residue: 0.5305 time to fit residues: 74.5861 Evaluate side-chains 124 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 252 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN B 82 GLN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.135832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.113501 restraints weight = 8308.780| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.49 r_work: 0.3455 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5637 Z= 0.135 Angle : 0.623 10.332 7641 Z= 0.299 Chirality : 0.044 0.254 881 Planarity : 0.004 0.037 952 Dihedral : 7.922 107.769 750 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.22 % Allowed : 21.27 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.33), residues: 670 helix: 1.14 (0.25), residues: 404 sheet: -0.23 (0.66), residues: 66 loop : 0.23 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 267 TYR 0.015 0.002 TYR C 83 PHE 0.022 0.002 PHE A 583 TRP 0.011 0.001 TRP C 130 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 5637) covalent geometry : angle 0.62278 / 0.30 ( 7641) hydrogen bonds : bond 0.03655 / 2.52 ( 307) hydrogen bonds : angle 4.79237 / 3.27 ( 903) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 459 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7661 (tt) REVERT: A 500 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7327 (mp10) REVERT: A 530 THR cc_start: 0.8593 (m) cc_final: 0.8393 (p) REVERT: A 595 ASN cc_start: 0.8081 (t0) cc_final: 0.7821 (t0) REVERT: B 51 TYR cc_start: 0.7533 (t80) cc_final: 0.7118 (t80) REVERT: B 101 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7080 (mtp180) REVERT: B 106 MET cc_start: 0.7601 (mmm) cc_final: 0.7322 (tpt) REVERT: B 107 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7435 (mmpt) REVERT: B 263 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7826 (tp30) REVERT: B 265 TYR cc_start: 0.7234 (t80) cc_final: 0.6535 (t80) REVERT: B 266 GLU cc_start: 0.7914 (tp30) cc_final: 0.7615 (tp30) REVERT: C 6 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: C 59 GLU cc_start: 0.7753 (mp0) cc_final: 0.7466 (pt0) REVERT: C 82 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7398 (mt-10) REVERT: C 120 MET cc_start: 0.7658 (mmp) cc_final: 0.7434 (mmm) REVERT: C 145 MET cc_start: 0.8124 (mmm) cc_final: 0.7638 (mtp) REVERT: C 192 ASP cc_start: 0.7700 (t0) cc_final: 0.7449 (t0) REVERT: C 195 MET cc_start: 0.7691 (mmm) cc_final: 0.7266 (mmp) REVERT: C 207 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.6173 (mpp-170) outliers start: 26 outliers final: 12 residues processed: 138 average time/residue: 0.5109 time to fit residues: 74.0197 Evaluate side-chains 125 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 252 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 25 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 3 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN A 543 ASN B 82 GLN B 88 ASN B 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.135349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.113031 restraints weight = 8458.506| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.52 r_work: 0.3445 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5637 Z= 0.150 Angle : 0.627 8.781 7641 Z= 0.306 Chirality : 0.044 0.249 881 Planarity : 0.004 0.050 952 Dihedral : 7.912 106.901 750 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 5.19 % Allowed : 20.45 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.33), residues: 670 helix: 1.11 (0.25), residues: 404 sheet: -0.44 (0.66), residues: 69 loop : 0.28 (0.49), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 267 TYR 0.015 0.002 TYR C 19 PHE 0.025 0.002 PHE A 583 TRP 0.012 0.001 TRP C 130 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 5637) covalent geometry : angle 0.62684 / 0.31 ( 7641) hydrogen bonds : bond 0.03731 / 2.57 ( 307) hydrogen bonds : angle 4.79765 / 3.27 ( 903) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 459 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7680 (mt) REVERT: A 595 ASN cc_start: 0.8097 (t0) cc_final: 0.7859 (t0) REVERT: B 51 TYR cc_start: 0.7510 (t80) cc_final: 0.7088 (t80) REVERT: B 106 MET cc_start: 0.7408 (mmm) cc_final: 0.7178 (mmp) REVERT: B 107 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7412 (mmpt) REVERT: B 263 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7926 (tp30) REVERT: B 265 TYR cc_start: 0.7267 (t80) cc_final: 0.6558 (t80) REVERT: B 266 GLU cc_start: 0.7914 (tp30) cc_final: 0.7587 (tp30) REVERT: C 6 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: C 59 GLU cc_start: 0.7785 (mp0) cc_final: 0.7473 (pt0) REVERT: C 82 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7405 (mt-10) REVERT: C 120 MET cc_start: 0.7685 (mmp) cc_final: 0.7477 (mmm) REVERT: C 145 MET cc_start: 0.8116 (mmm) cc_final: 0.7562 (mtp) REVERT: C 192 ASP cc_start: 0.7807 (t0) cc_final: 0.7534 (t0) REVERT: C 195 MET cc_start: 0.7726 (mmm) cc_final: 0.7362 (mmp) REVERT: C 207 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6258 (mpp-170) outliers start: 32 outliers final: 12 residues processed: 125 average time/residue: 0.5161 time to fit residues: 67.5836 Evaluate side-chains 117 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 252 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN A 543 ASN B 82 GLN B 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.132328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109717 restraints weight = 8346.707| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.51 r_work: 0.3382 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5637 Z= 0.154 Angle : 0.625 6.849 7641 Z= 0.307 Chirality : 0.044 0.218 881 Planarity : 0.004 0.050 952 Dihedral : 7.914 106.322 750 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.71 % Allowed : 21.43 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.34), residues: 670 helix: 1.06 (0.25), residues: 405 sheet: -0.42 (0.66), residues: 69 loop : 0.39 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 267 TYR 0.013 0.002 TYR A 387 PHE 0.032 0.002 PHE A 583 TRP 0.011 0.001 TRP C 130 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 5637) covalent geometry : angle 0.62527 / 0.31 ( 7641) hydrogen bonds : bond 0.03760 / 2.57 ( 307) hydrogen bonds : angle 4.77758 / 3.26 ( 903) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 459 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7690 (mt) REVERT: A 500 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7252 (mp10) REVERT: A 582 ARG cc_start: 0.8566 (mtm110) cc_final: 0.8145 (mtm110) REVERT: A 595 ASN cc_start: 0.8103 (t0) cc_final: 0.7841 (t0) REVERT: B 51 TYR cc_start: 0.7493 (t80) cc_final: 0.7083 (t80) REVERT: B 107 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7330 (mmpt) REVERT: B 123 THR cc_start: 0.8421 (p) cc_final: 0.8083 (p) REVERT: B 263 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7925 (tp30) REVERT: B 266 GLU cc_start: 0.7971 (tp30) cc_final: 0.7696 (tp30) REVERT: C 6 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7930 (mt0) REVERT: C 44 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7564 (mt-10) REVERT: C 59 GLU cc_start: 0.7762 (mp0) cc_final: 0.7456 (pt0) REVERT: C 82 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7461 (mt-10) REVERT: C 145 MET cc_start: 0.8252 (mmm) cc_final: 0.7667 (mtp) REVERT: C 192 ASP cc_start: 0.7840 (t0) cc_final: 0.7322 (t0) REVERT: C 207 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.6364 (mpp-170) outliers start: 29 outliers final: 14 residues processed: 133 average time/residue: 0.5128 time to fit residues: 71.4428 Evaluate side-chains 121 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 252 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN A 592 HIS B 88 ASN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.109862 restraints weight = 8322.764| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.56 r_work: 0.3388 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5637 Z= 0.162 Angle : 0.676 8.955 7641 Z= 0.329 Chirality : 0.045 0.277 881 Planarity : 0.005 0.057 952 Dihedral : 7.907 105.820 750 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.22 % Allowed : 22.73 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.33), residues: 670 helix: 1.12 (0.25), residues: 404 sheet: -0.45 (0.65), residues: 70 loop : 0.16 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 229 TYR 0.017 0.002 TYR B 265 PHE 0.026 0.002 PHE A 583 TRP 0.013 0.001 TRP C 130 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 5637) covalent geometry : angle 0.67582 / 0.33 ( 7641) hydrogen bonds : bond 0.03699 / 2.55 ( 307) hydrogen bonds : angle 4.80931 / 3.27 ( 903) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.161 Fit side-chains REVERT: A 457 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6770 (mt-10) REVERT: A 459 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7731 (mt) REVERT: A 500 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7267 (mp10) REVERT: A 508 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7562 (pp20) REVERT: A 582 ARG cc_start: 0.8490 (mtm110) cc_final: 0.8155 (mtm110) REVERT: A 595 ASN cc_start: 0.8092 (t0) cc_final: 0.7822 (t0) REVERT: B 51 TYR cc_start: 0.7471 (t80) cc_final: 0.7073 (t80) REVERT: B 107 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7390 (mmpt) REVERT: B 123 THR cc_start: 0.8407 (p) cc_final: 0.8069 (p) REVERT: B 263 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7982 (tp30) REVERT: B 265 TYR cc_start: 0.7170 (t80) cc_final: 0.6750 (t80) REVERT: B 266 GLU cc_start: 0.7969 (tp30) cc_final: 0.7640 (tp30) REVERT: C 6 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: C 44 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7444 (mt-10) REVERT: C 82 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7436 (mt-10) REVERT: C 145 MET cc_start: 0.8247 (mmm) cc_final: 0.7647 (mtp) REVERT: C 192 ASP cc_start: 0.7640 (t70) cc_final: 0.7286 (t0) REVERT: C 207 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6376 (mpp-170) outliers start: 26 outliers final: 13 residues processed: 124 average time/residue: 0.5054 time to fit residues: 65.7186 Evaluate side-chains 120 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 252 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.0170 chunk 20 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN A 592 HIS B 42 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.134668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.112297 restraints weight = 8331.995| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.51 r_work: 0.3417 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5637 Z= 0.142 Angle : 0.667 9.584 7641 Z= 0.326 Chirality : 0.044 0.302 881 Planarity : 0.005 0.061 952 Dihedral : 7.752 103.442 750 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.60 % Allowed : 24.35 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.33), residues: 670 helix: 1.11 (0.25), residues: 410 sheet: -0.50 (0.65), residues: 70 loop : 0.22 (0.50), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 229 TYR 0.021 0.002 TYR C 19 PHE 0.020 0.002 PHE C 88 TRP 0.010 0.001 TRP C 130 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 5637) covalent geometry : angle 0.66676 / 0.33 ( 7641) hydrogen bonds : bond 0.03508 / 2.40 ( 307) hydrogen bonds : angle 4.81599 / 3.30 ( 903) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 457 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6771 (mt-10) REVERT: A 459 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7719 (mt) REVERT: A 500 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7287 (mp10) REVERT: A 595 ASN cc_start: 0.8096 (t0) cc_final: 0.7864 (t0) REVERT: B 51 TYR cc_start: 0.7449 (t80) cc_final: 0.7055 (t80) REVERT: B 107 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7408 (mmpt) REVERT: B 230 VAL cc_start: 0.8221 (p) cc_final: 0.7997 (t) REVERT: B 263 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7960 (tp30) REVERT: B 265 TYR cc_start: 0.7266 (t80) cc_final: 0.6863 (t80) REVERT: B 266 GLU cc_start: 0.7934 (tp30) cc_final: 0.7592 (tp30) REVERT: C 6 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: C 44 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7196 (mt-10) REVERT: C 82 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7428 (mt-10) REVERT: C 145 MET cc_start: 0.8200 (mmm) cc_final: 0.7682 (mtp) REVERT: C 207 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.6295 (mpp-170) outliers start: 16 outliers final: 11 residues processed: 122 average time/residue: 0.4705 time to fit residues: 60.3459 Evaluate side-chains 120 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 252 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 0.0570 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN A 592 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.133639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.109930 restraints weight = 8404.915| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.60 r_work: 0.3395 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5637 Z= 0.157 Angle : 0.712 9.103 7641 Z= 0.348 Chirality : 0.045 0.263 881 Planarity : 0.005 0.057 952 Dihedral : 7.744 103.681 750 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.08 % Allowed : 24.84 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.34), residues: 670 helix: 1.09 (0.25), residues: 411 sheet: -0.56 (0.65), residues: 70 loop : 0.22 (0.51), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 582 TYR 0.017 0.002 TYR C 83 PHE 0.025 0.002 PHE A 583 TRP 0.011 0.001 TRP C 130 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 5637) covalent geometry : angle 0.71243 / 0.35 ( 7641) hydrogen bonds : bond 0.03618 / 2.47 ( 307) hydrogen bonds : angle 4.81613 / 3.30 ( 903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2340.10 seconds wall clock time: 40 minutes 35.17 seconds (2435.17 seconds total)