Starting phenix.real_space_refine on Tue Feb 3 22:32:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r1e_53506/02_2026/9r1e_53506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r1e_53506/02_2026/9r1e_53506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r1e_53506/02_2026/9r1e_53506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r1e_53506/02_2026/9r1e_53506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r1e_53506/02_2026/9r1e_53506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r1e_53506/02_2026/9r1e_53506.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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 32 5.16 5 C 4824 2.51 5 N 1167 2.21 5 O 1306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7329 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3724 Classifications: {'peptide': 486} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 475} Chain breaks: 1 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: "H" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1707 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 215} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1628 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "A" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 237 Unusual residues: {'CLR': 8, 'WRF': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 3} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.74, per 1000 atoms: 0.24 Number of scatterers: 7329 At special positions: 0 Unit cell: (76.7, 68.9, 143.65, 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 32 16.00 O 1306 8.00 N 1167 7.00 C 4824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 283.3 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 52.5% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 27 through 62 removed outlier: 3.571A pdb=" N GLU A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Proline residue: A 44 - end of helix removed outlier: 4.095A pdb=" N SER A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 68 through 85 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.570A pdb=" N LEU A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 removed outlier: 5.496A pdb=" N LYS A 110 " --> pdb=" O GLN A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 111 through 136 removed outlier: 4.095A pdb=" N PHE A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 3.541A pdb=" N ASN A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 147 through 161 removed outlier: 3.583A pdb=" N ARG A 152 " --> pdb=" O PRO A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 180 removed outlier: 4.431A pdb=" N ALA A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 207 Processing helix chain 'A' and resid 212 through 238 Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.548A pdb=" N CYS A 252 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 288 removed outlier: 3.584A pdb=" N PHE A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 4.231A pdb=" N MET A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 326 removed outlier: 4.508A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 328 through 357 Processing helix chain 'A' and resid 357 through 366 removed outlier: 4.227A pdb=" N GLY A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE A 364 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 402 Proline residue: A 380 - end of helix removed outlier: 4.028A pdb=" N LEU A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.695A pdb=" N GLY A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 431 Processing helix chain 'A' and resid 434 through 459 removed outlier: 3.813A pdb=" N LEU A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'A' and resid 538 through 567 Processing helix chain 'H' and resid 84 through 88 removed outlier: 4.112A pdb=" N THR H 88 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 107 removed outlier: 3.957A pdb=" N PHE H 106 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 198 through 203 removed outlier: 3.809A pdb=" N GLN H 203 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.714A pdb=" N SER L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.505A pdb=" N TYR H 91 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 17 through 21 Processing sheet with id=AA4, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.792A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.792A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.524A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR H 205 " --> pdb=" O VAL H 222 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.573A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.502A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER L 176 " --> pdb=" O SER L 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.742A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1251 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: 0.97 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2209 1.34 - 1.46: 1653 1.46 - 1.58: 3606 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 7512 Sorted by residual: bond pdb=" C05 WRF A 601 " pdb=" C08 WRF A 601 " ideal model delta sigma weight residual 1.470 1.321 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" C05 WRF A 601 " pdb=" C06 WRF A 601 " ideal model delta sigma weight residual 1.403 1.375 0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" C01 WRF A 601 " pdb=" N02 WRF A 601 " ideal model delta sigma weight residual 1.475 1.451 0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" CA GLN L 3 " pdb=" CB GLN L 3 " ideal model delta sigma weight residual 1.532 1.550 -0.018 1.48e-02 4.57e+03 1.47e+00 bond pdb=" C GLY A 67 " pdb=" O GLY A 67 " ideal model delta sigma weight residual 1.237 1.229 0.008 7.00e-03 2.04e+04 1.47e+00 ... (remaining 7507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 10138 1.78 - 3.57: 115 3.57 - 5.35: 22 5.35 - 7.13: 6 7.13 - 8.91: 1 Bond angle restraints: 10282 Sorted by residual: angle pdb=" N VAL A 419 " pdb=" CA VAL A 419 " pdb=" C VAL A 419 " ideal model delta sigma weight residual 113.53 108.39 5.14 9.80e-01 1.04e+00 2.75e+01 angle pdb=" CA GLN L 3 " pdb=" CB GLN L 3 " pdb=" CG GLN L 3 " ideal model delta sigma weight residual 114.10 120.92 -6.82 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA VAL A 419 " pdb=" C VAL A 419 " pdb=" N GLY A 420 " ideal model delta sigma weight residual 119.31 116.20 3.11 1.15e+00 7.56e-01 7.31e+00 angle pdb=" CA LEU A 250 " pdb=" CB LEU A 250 " pdb=" CG LEU A 250 " ideal model delta sigma weight residual 116.30 125.21 -8.91 3.50e+00 8.16e-02 6.48e+00 angle pdb=" C GLN L 3 " pdb=" CA GLN L 3 " pdb=" CB GLN L 3 " ideal model delta sigma weight residual 112.11 115.48 -3.37 1.46e+00 4.69e-01 5.34e+00 ... (remaining 10277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4176 17.13 - 34.26: 465 34.26 - 51.38: 137 51.38 - 68.51: 30 68.51 - 85.64: 5 Dihedral angle restraints: 4813 sinusoidal: 2148 harmonic: 2665 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual 93.00 46.74 46.26 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" CB CYS H 151 " pdb=" SG CYS H 151 " pdb=" SG CYS H 207 " pdb=" CB CYS H 207 " ideal model delta sinusoidal sigma weight residual 93.00 47.70 45.30 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 136.12 -43.12 1 1.00e+01 1.00e-02 2.59e+01 ... (remaining 4810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 840 0.033 - 0.067: 290 0.067 - 0.100: 71 0.100 - 0.134: 29 0.134 - 0.167: 3 Chirality restraints: 1233 Sorted by residual: chirality pdb=" C20 CLR A 604 " pdb=" C17 CLR A 604 " pdb=" C21 CLR A 604 " pdb=" C22 CLR A 604 " both_signs ideal model delta sigma weight residual False 2.59 2.43 0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" C17 CLR A 604 " pdb=" C13 CLR A 604 " pdb=" C16 CLR A 604 " pdb=" C20 CLR A 604 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA VAL L 58 " pdb=" N VAL L 58 " pdb=" C VAL L 58 " pdb=" CB VAL L 58 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 1230 not shown) Planarity restraints: 1217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 43 " 0.035 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO L 44 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO L 40 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 203 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO L 204 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO L 204 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 204 " -0.025 5.00e-02 4.00e+02 ... (remaining 1214 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1042 2.75 - 3.29: 6917 3.29 - 3.83: 11872 3.83 - 4.36: 13965 4.36 - 4.90: 25241 Nonbonded interactions: 59037 Sorted by model distance: nonbonded pdb=" OH TYR A 277 " pdb=" OE2 GLU A 389 " model vdw 2.219 3.040 nonbonded pdb=" OG SER A 402 " pdb=" OD1 ASN A 404 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 177 " pdb=" OG1 THR A 244 " model vdw 2.226 3.040 nonbonded pdb=" O SER H 32 " pdb=" OG SER H 53 " model vdw 2.249 3.040 nonbonded pdb=" OG SER H 197 " pdb=" N SER H 198 " model vdw 2.295 3.120 ... (remaining 59032 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: 6.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.003 0.149 7518 Z= 0.152 Angle : 0.546 8.913 10290 Z= 0.285 Chirality : 0.039 0.167 1233 Planarity : 0.004 0.054 1217 Dihedral : 15.428 85.638 3095 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.26 % Favored : 95.63 % Rotamer: Outliers : 3.23 % Allowed : 25.29 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.03 (0.29), residues: 916 helix: 2.06 (0.25), residues: 425 sheet: 0.12 (0.41), residues: 182 loop : -0.91 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.014 0.001 TYR A 203 PHE 0.009 0.001 PHE A 282 TRP 0.011 0.001 TRP A 439 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7512) covalent geometry : angle 0.54554 (10282) SS BOND : bond 0.00216 ( 4) SS BOND : angle 0.51453 ( 8) hydrogen bonds : bond 0.17886 ( 428) hydrogen bonds : angle 7.23870 ( 1251) Misc. bond : bond 0.00096 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 239 LYS cc_start: 0.8573 (mttt) cc_final: 0.8157 (mttp) REVERT: A 459 GLN cc_start: 0.7826 (pp30) cc_final: 0.7530 (pp30) REVERT: H 11 LEU cc_start: 0.8989 (tp) cc_final: 0.8743 (mt) REVERT: H 203 GLN cc_start: 0.5318 (OUTLIER) cc_final: 0.4244 (pm20) REVERT: H 207 CYS cc_start: 0.7620 (t) cc_final: 0.7409 (t) REVERT: L 3 GLN cc_start: 0.8394 (pt0) cc_final: 0.7966 (tm-30) REVERT: L 18 ARG cc_start: 0.8624 (mtp-110) cc_final: 0.8381 (ttt90) REVERT: L 45 LYS cc_start: 0.8630 (mtmm) cc_final: 0.7907 (mttm) outliers start: 25 outliers final: 24 residues processed: 101 average time/residue: 0.0694 time to fit residues: 9.8295 Evaluate side-chains 103 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 202 ASN A 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.143866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111850 restraints weight = 9281.628| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.12 r_work: 0.3099 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 7518 Z= 0.314 Angle : 0.719 9.123 10290 Z= 0.363 Chirality : 0.046 0.167 1233 Planarity : 0.005 0.047 1217 Dihedral : 7.867 55.100 1615 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.13 % Favored : 94.76 % Rotamer: Outliers : 7.23 % Allowed : 22.45 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.74 (0.28), residues: 916 helix: 1.65 (0.24), residues: 431 sheet: 0.31 (0.40), residues: 177 loop : -1.04 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 66 TYR 0.022 0.003 TYR A 277 PHE 0.018 0.002 PHE L 139 TRP 0.012 0.002 TRP A 439 HIS 0.004 0.002 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00754 ( 7512) covalent geometry : angle 0.71902 (10282) SS BOND : bond 0.00508 ( 4) SS BOND : angle 1.03544 ( 8) hydrogen bonds : bond 0.05507 ( 428) hydrogen bonds : angle 5.42186 ( 1251) Misc. bond : bond 0.00098 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 82 time to evaluate : 0.202 Fit side-chains REVERT: A 239 LYS cc_start: 0.8570 (mttt) cc_final: 0.8071 (mttp) REVERT: A 353 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7782 (tt) REVERT: A 459 GLN cc_start: 0.7744 (pp30) cc_final: 0.7371 (pp30) REVERT: H 203 GLN cc_start: 0.5462 (OUTLIER) cc_final: 0.4376 (pm20) REVERT: L 3 GLN cc_start: 0.8539 (pt0) cc_final: 0.8128 (tm-30) REVERT: L 45 LYS cc_start: 0.8557 (mtmm) cc_final: 0.7845 (mttm) REVERT: L 149 LYS cc_start: 0.7406 (mmmt) cc_final: 0.7179 (mtpp) outliers start: 56 outliers final: 44 residues processed: 130 average time/residue: 0.0674 time to fit residues: 12.4146 Evaluate side-chains 119 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 73 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 82 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.148061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116861 restraints weight = 9096.676| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.06 r_work: 0.3163 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7518 Z= 0.148 Angle : 0.571 6.843 10290 Z= 0.288 Chirality : 0.040 0.167 1233 Planarity : 0.004 0.047 1217 Dihedral : 7.308 58.937 1602 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.80 % Favored : 95.09 % Rotamer: Outliers : 6.58 % Allowed : 23.74 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.17 (0.29), residues: 916 helix: 2.08 (0.25), residues: 431 sheet: 0.55 (0.40), residues: 176 loop : -0.99 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.017 0.002 TYR A 306 PHE 0.010 0.001 PHE A 282 TRP 0.014 0.001 TRP A 439 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7512) covalent geometry : angle 0.57107 (10282) SS BOND : bond 0.00837 ( 4) SS BOND : angle 0.66980 ( 8) hydrogen bonds : bond 0.04544 ( 428) hydrogen bonds : angle 4.93597 ( 1251) Misc. bond : bond 0.00056 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 82 time to evaluate : 0.193 Fit side-chains REVERT: A 239 LYS cc_start: 0.8539 (mttt) cc_final: 0.8028 (mttp) REVERT: A 353 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7398 (mt) REVERT: H 55 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7134 (p90) REVERT: H 138 SER cc_start: 0.6564 (OUTLIER) cc_final: 0.6309 (t) REVERT: H 203 GLN cc_start: 0.5391 (OUTLIER) cc_final: 0.4300 (pm20) REVERT: H 207 CYS cc_start: 0.7581 (t) cc_final: 0.7368 (t) REVERT: H 221 LYS cc_start: 0.8399 (mppt) cc_final: 0.7787 (tttt) REVERT: L 3 GLN cc_start: 0.8388 (pt0) cc_final: 0.7880 (tm-30) REVERT: L 143 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: L 149 LYS cc_start: 0.7366 (mmmt) cc_final: 0.7154 (mtpp) outliers start: 51 outliers final: 38 residues processed: 123 average time/residue: 0.0683 time to fit residues: 11.8133 Evaluate side-chains 121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 78 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.150291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119063 restraints weight = 9237.891| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.08 r_work: 0.3190 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7518 Z= 0.120 Angle : 0.538 6.020 10290 Z= 0.272 Chirality : 0.039 0.167 1233 Planarity : 0.004 0.046 1217 Dihedral : 6.939 59.929 1597 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.48 % Favored : 95.41 % Rotamer: Outliers : 5.94 % Allowed : 24.26 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.52 (0.29), residues: 916 helix: 2.35 (0.25), residues: 431 sheet: 0.77 (0.41), residues: 176 loop : -0.83 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.015 0.001 TYR A 306 PHE 0.011 0.001 PHE A 456 TRP 0.013 0.001 TRP A 439 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7512) covalent geometry : angle 0.53817 (10282) SS BOND : bond 0.00242 ( 4) SS BOND : angle 0.57536 ( 8) hydrogen bonds : bond 0.04031 ( 428) hydrogen bonds : angle 4.59536 ( 1251) Misc. bond : bond 0.00053 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 83 time to evaluate : 0.305 Fit side-chains REVERT: A 239 LYS cc_start: 0.8530 (mttt) cc_final: 0.8059 (mttp) REVERT: A 353 LEU cc_start: 0.7928 (tt) cc_final: 0.7383 (mt) REVERT: H 48 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8400 (m) REVERT: H 60 TYR cc_start: 0.8196 (m-80) cc_final: 0.7604 (m-80) REVERT: H 138 SER cc_start: 0.6558 (OUTLIER) cc_final: 0.6214 (p) REVERT: H 171 THR cc_start: 0.7822 (OUTLIER) cc_final: 0.7404 (t) REVERT: H 203 GLN cc_start: 0.5421 (OUTLIER) cc_final: 0.4331 (pm20) REVERT: H 221 LYS cc_start: 0.8322 (mppt) cc_final: 0.7823 (tttt) REVERT: L 3 GLN cc_start: 0.8351 (pt0) cc_final: 0.7789 (tm-30) REVERT: L 143 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7992 (mp0) outliers start: 46 outliers final: 36 residues processed: 119 average time/residue: 0.0649 time to fit residues: 11.5199 Evaluate side-chains 121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 22 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.148392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117294 restraints weight = 9162.911| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.08 r_work: 0.3167 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7518 Z= 0.151 Angle : 0.561 5.929 10290 Z= 0.283 Chirality : 0.040 0.167 1233 Planarity : 0.004 0.046 1217 Dihedral : 6.966 59.918 1594 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 6.84 % Allowed : 23.74 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.54 (0.29), residues: 916 helix: 2.32 (0.24), residues: 431 sheet: 0.84 (0.41), residues: 177 loop : -0.77 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 66 TYR 0.016 0.002 TYR A 306 PHE 0.010 0.001 PHE L 139 TRP 0.011 0.001 TRP A 439 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7512) covalent geometry : angle 0.56049 (10282) SS BOND : bond 0.00333 ( 4) SS BOND : angle 1.02730 ( 8) hydrogen bonds : bond 0.04265 ( 428) hydrogen bonds : angle 4.59444 ( 1251) Misc. bond : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 82 time to evaluate : 0.185 Fit side-chains REVERT: A 239 LYS cc_start: 0.8529 (mttt) cc_final: 0.8053 (mttp) REVERT: A 353 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7386 (mt) REVERT: H 48 VAL cc_start: 0.8662 (OUTLIER) cc_final: 0.8444 (m) REVERT: H 60 TYR cc_start: 0.8196 (m-80) cc_final: 0.7612 (m-80) REVERT: H 138 SER cc_start: 0.6573 (OUTLIER) cc_final: 0.6240 (p) REVERT: H 171 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7498 (t) REVERT: H 203 GLN cc_start: 0.5555 (OUTLIER) cc_final: 0.4442 (pm20) REVERT: L 3 GLN cc_start: 0.8354 (pt0) cc_final: 0.7753 (tm-30) REVERT: L 143 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: L 149 LYS cc_start: 0.7474 (mmmt) cc_final: 0.7208 (mtpp) outliers start: 53 outliers final: 40 residues processed: 122 average time/residue: 0.0594 time to fit residues: 10.6280 Evaluate side-chains 126 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 80 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 28 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.0270 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.151380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121026 restraints weight = 9217.473| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.04 r_work: 0.3218 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7518 Z= 0.133 Angle : 0.553 8.447 10290 Z= 0.277 Chirality : 0.040 0.168 1233 Planarity : 0.004 0.045 1217 Dihedral : 6.838 59.270 1594 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.48 % Favored : 95.41 % Rotamer: Outliers : 5.94 % Allowed : 23.87 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.63 (0.29), residues: 916 helix: 2.36 (0.24), residues: 431 sheet: 0.94 (0.41), residues: 176 loop : -0.70 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 36 TYR 0.016 0.001 TYR A 306 PHE 0.010 0.001 PHE A 456 TRP 0.012 0.001 TRP A 439 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7512) covalent geometry : angle 0.55244 (10282) SS BOND : bond 0.00291 ( 4) SS BOND : angle 0.92660 ( 8) hydrogen bonds : bond 0.04111 ( 428) hydrogen bonds : angle 4.48562 ( 1251) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 84 time to evaluate : 0.196 Fit side-chains REVERT: A 239 LYS cc_start: 0.8552 (mttt) cc_final: 0.8094 (mttp) REVERT: A 353 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7512 (mt) REVERT: A 565 PHE cc_start: 0.6819 (m-80) cc_final: 0.6556 (m-80) REVERT: H 55 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7279 (p90) REVERT: H 60 TYR cc_start: 0.8063 (m-80) cc_final: 0.7622 (m-80) REVERT: H 138 SER cc_start: 0.6418 (OUTLIER) cc_final: 0.6116 (p) REVERT: H 171 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7541 (t) REVERT: H 203 GLN cc_start: 0.5652 (OUTLIER) cc_final: 0.4448 (pm20) REVERT: L 3 GLN cc_start: 0.8339 (pt0) cc_final: 0.7810 (tm-30) REVERT: L 124 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.4850 (tp40) REVERT: L 143 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8132 (mp0) outliers start: 46 outliers final: 35 residues processed: 119 average time/residue: 0.0580 time to fit residues: 10.3242 Evaluate side-chains 120 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 78 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 88 optimal weight: 0.0040 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121512 restraints weight = 9239.616| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.11 r_work: 0.3241 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7518 Z= 0.124 Angle : 0.536 6.953 10290 Z= 0.270 Chirality : 0.039 0.168 1233 Planarity : 0.004 0.046 1217 Dihedral : 6.635 58.423 1590 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.37 % Favored : 95.52 % Rotamer: Outliers : 5.68 % Allowed : 23.87 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.75 (0.29), residues: 916 helix: 2.46 (0.24), residues: 429 sheet: 0.99 (0.41), residues: 176 loop : -0.64 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 67 TYR 0.015 0.001 TYR A 306 PHE 0.011 0.001 PHE A 456 TRP 0.012 0.001 TRP A 439 HIS 0.002 0.001 HIS H 211 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7512) covalent geometry : angle 0.53611 (10282) SS BOND : bond 0.00422 ( 4) SS BOND : angle 0.75009 ( 8) hydrogen bonds : bond 0.03961 ( 428) hydrogen bonds : angle 4.37091 ( 1251) Misc. bond : bond 0.00054 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 86 time to evaluate : 0.263 Fit side-chains REVERT: A 239 LYS cc_start: 0.8544 (mttt) cc_final: 0.8077 (mttp) REVERT: A 353 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7449 (mt) REVERT: A 565 PHE cc_start: 0.6814 (m-80) cc_final: 0.6513 (m-80) REVERT: H 55 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7305 (p90) REVERT: H 60 TYR cc_start: 0.7998 (m-80) cc_final: 0.7661 (m-80) REVERT: H 138 SER cc_start: 0.6425 (OUTLIER) cc_final: 0.6149 (p) REVERT: H 171 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7539 (t) REVERT: H 203 GLN cc_start: 0.5754 (OUTLIER) cc_final: 0.5507 (pm20) REVERT: L 3 GLN cc_start: 0.8307 (pt0) cc_final: 0.7781 (tm-30) REVERT: L 124 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.4883 (tp40) REVERT: L 143 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8112 (mp0) outliers start: 44 outliers final: 32 residues processed: 120 average time/residue: 0.0674 time to fit residues: 11.8476 Evaluate side-chains 121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.148116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118309 restraints weight = 9366.107| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.11 r_work: 0.3195 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7518 Z= 0.175 Angle : 0.583 6.512 10290 Z= 0.293 Chirality : 0.041 0.167 1233 Planarity : 0.004 0.046 1217 Dihedral : 6.890 59.122 1589 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 6.71 % Allowed : 23.35 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.55 (0.29), residues: 916 helix: 2.25 (0.24), residues: 429 sheet: 0.92 (0.40), residues: 177 loop : -0.66 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 211 TYR 0.016 0.002 TYR A 277 PHE 0.013 0.001 PHE L 139 TRP 0.010 0.001 TRP A 439 HIS 0.002 0.001 HIS A 386 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7512) covalent geometry : angle 0.58283 (10282) SS BOND : bond 0.00401 ( 4) SS BOND : angle 0.93319 ( 8) hydrogen bonds : bond 0.04418 ( 428) hydrogen bonds : angle 4.50631 ( 1251) Misc. bond : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 79 time to evaluate : 0.176 Fit side-chains REVERT: A 239 LYS cc_start: 0.8561 (mttt) cc_final: 0.8099 (mttp) REVERT: A 353 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7603 (mt) REVERT: H 60 TYR cc_start: 0.8087 (m-80) cc_final: 0.7663 (m-80) REVERT: H 138 SER cc_start: 0.6559 (OUTLIER) cc_final: 0.6280 (p) REVERT: H 171 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7622 (t) REVERT: H 203 GLN cc_start: 0.5833 (OUTLIER) cc_final: 0.5456 (pt0) REVERT: L 3 GLN cc_start: 0.8375 (pt0) cc_final: 0.7864 (tm-30) REVERT: L 124 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.4909 (tp40) REVERT: L 143 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: L 149 LYS cc_start: 0.7532 (mmmt) cc_final: 0.7316 (mtpt) outliers start: 52 outliers final: 40 residues processed: 117 average time/residue: 0.0624 time to fit residues: 10.9940 Evaluate side-chains 124 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 78 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 81 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.149191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117684 restraints weight = 9107.241| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.16 r_work: 0.3229 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7518 Z= 0.134 Angle : 0.548 6.548 10290 Z= 0.277 Chirality : 0.040 0.169 1233 Planarity : 0.004 0.047 1217 Dihedral : 6.675 58.679 1589 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.91 % Favored : 94.98 % Rotamer: Outliers : 5.81 % Allowed : 24.26 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.70 (0.29), residues: 916 helix: 2.39 (0.24), residues: 429 sheet: 1.06 (0.41), residues: 176 loop : -0.66 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 67 TYR 0.015 0.001 TYR A 306 PHE 0.011 0.001 PHE A 456 TRP 0.012 0.001 TRP A 439 HIS 0.002 0.001 HIS H 211 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7512) covalent geometry : angle 0.54734 (10282) SS BOND : bond 0.00380 ( 4) SS BOND : angle 0.76096 ( 8) hydrogen bonds : bond 0.04071 ( 428) hydrogen bonds : angle 4.39747 ( 1251) Misc. bond : bond 0.00054 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 78 time to evaluate : 0.312 Fit side-chains REVERT: A 239 LYS cc_start: 0.8570 (mttt) cc_final: 0.8067 (mttp) REVERT: A 353 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7586 (mt) REVERT: H 55 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7349 (p90) REVERT: H 60 TYR cc_start: 0.7977 (m-80) cc_final: 0.7759 (m-80) REVERT: H 138 SER cc_start: 0.6527 (OUTLIER) cc_final: 0.6260 (p) REVERT: H 171 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7669 (t) REVERT: L 3 GLN cc_start: 0.8291 (pt0) cc_final: 0.7782 (tm-30) REVERT: L 124 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.4932 (tp40) REVERT: L 143 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: L 149 LYS cc_start: 0.7578 (mmmt) cc_final: 0.7313 (mtpt) outliers start: 45 outliers final: 37 residues processed: 111 average time/residue: 0.0585 time to fit residues: 9.7005 Evaluate side-chains 120 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121513 restraints weight = 9200.467| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.97 r_work: 0.3243 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7518 Z= 0.121 Angle : 0.534 6.630 10290 Z= 0.270 Chirality : 0.039 0.169 1233 Planarity : 0.004 0.047 1217 Dihedral : 6.407 59.334 1585 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 5.42 % Allowed : 25.03 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.79 (0.29), residues: 916 helix: 2.47 (0.24), residues: 429 sheet: 1.16 (0.41), residues: 176 loop : -0.65 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 95 TYR 0.015 0.001 TYR A 306 PHE 0.012 0.001 PHE A 456 TRP 0.011 0.001 TRP A 439 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7512) covalent geometry : angle 0.53375 (10282) SS BOND : bond 0.00367 ( 4) SS BOND : angle 0.73680 ( 8) hydrogen bonds : bond 0.03911 ( 428) hydrogen bonds : angle 4.27640 ( 1251) Misc. bond : bond 0.00049 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.275 Fit side-chains REVERT: A 239 LYS cc_start: 0.8551 (mttt) cc_final: 0.8090 (mttp) REVERT: A 353 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7586 (mt) REVERT: H 55 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7347 (p90) REVERT: H 138 SER cc_start: 0.6485 (OUTLIER) cc_final: 0.6250 (p) REVERT: H 171 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7624 (t) REVERT: L 3 GLN cc_start: 0.8240 (pt0) cc_final: 0.7799 (tm-30) REVERT: L 124 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.4824 (tp40) REVERT: L 143 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8149 (mp0) outliers start: 42 outliers final: 36 residues processed: 112 average time/residue: 0.0651 time to fit residues: 10.9738 Evaluate side-chains 121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 79 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.151124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121220 restraints weight = 9154.133| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.99 r_work: 0.3223 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7518 Z= 0.148 Angle : 0.556 6.572 10290 Z= 0.280 Chirality : 0.040 0.168 1233 Planarity : 0.004 0.047 1217 Dihedral : 6.529 58.965 1585 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.69 % Favored : 95.20 % Rotamer: Outliers : 5.68 % Allowed : 24.90 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.74 (0.29), residues: 916 helix: 2.40 (0.24), residues: 429 sheet: 1.17 (0.41), residues: 176 loop : -0.67 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 67 TYR 0.033 0.002 TYR H 60 PHE 0.010 0.001 PHE A 456 TRP 0.011 0.001 TRP A 439 HIS 0.002 0.001 HIS H 211 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7512) covalent geometry : angle 0.55582 (10282) SS BOND : bond 0.00388 ( 4) SS BOND : angle 0.79418 ( 8) hydrogen bonds : bond 0.04094 ( 428) hydrogen bonds : angle 4.34210 ( 1251) Misc. bond : bond 0.00058 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2088.45 seconds wall clock time: 36 minutes 34.49 seconds (2194.49 seconds total)