Starting phenix.real_space_refine on Thu Jul 2 09:15:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sp7_25367/07_2026/7sp7_25367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sp7_25367/07_2026/7sp7_25367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sp7_25367/07_2026/7sp7_25367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sp7_25367/07_2026/7sp7_25367.map" model { file = "/net/cci-nas-00/data/ceres_data/7sp7_25367/07_2026/7sp7_25367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sp7_25367/07_2026/7sp7_25367.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sp7_25367/07_2026/7sp7_25367.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sp7_25367/07_2026/7sp7_25367.cif" } resolution = 3.1 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1820 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 3 5.49 5 S 35 5.16 5 C 3914 2.51 5 N 991 2.21 5 O 1107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6052 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 497, 4053 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 13, 'TRANS': 483} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 497, 4053 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 13, 'TRANS': 483} Chain breaks: 1 bond proxies already assigned to first conformer: 4152 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 950 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 925 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MN': 2, '3PE': 1, 'UDP': 1, 'Y01': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 303 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 303 " occ=0.50 Time building chain proxies: 1.77, per 1000 atoms: 0.29 Number of scatterers: 6052 At special positions: 0 Unit cell: (71.28, 73.44, 154.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 35 16.00 P 3 15.00 O 1107 8.00 N 991 7.00 C 3914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 402.7 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1372 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 46.7% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 38 through 74 removed outlier: 3.683A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.968A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.044A pdb=" N THR A 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.510A pdb=" N TYR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Proline residue: A 217 - end of helix removed outlier: 3.502A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 3.634A pdb=" N TRP A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 5.337A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 300 through 312 removed outlier: 3.982A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 358 removed outlier: 4.542A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 364 through 392 Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.811A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 448 removed outlier: 3.778A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 470 through 497 removed outlier: 6.382A pdb=" N ILE A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 535 Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.538A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.554A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 3.773A pdb=" N ILE A 168 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA A 85 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE A 200 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 87 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 273 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 229 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.695A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.459A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.621A pdb=" N VAL B 12 " --> pdb=" O SER B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.814A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 97 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 113 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.814A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.795A pdb=" N ALA C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET C 82 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.795A pdb=" N ALA C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 58 through 59 removed outlier: 5.877A pdb=" N PHE C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG C 38 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 931 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: 0.82 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 935 1.28 - 1.41: 1717 1.41 - 1.55: 3459 1.55 - 1.68: 38 1.68 - 1.81: 54 Bond restraints: 6203 Sorted by residual: bond pdb=" C3' UDP A 603 " pdb=" C2' UDP A 603 " ideal model delta sigma weight residual 1.530 1.300 0.230 1.30e-02 5.92e+03 3.14e+02 bond pdb=" C5 UDP A 603 " pdb=" C6 UDP A 603 " ideal model delta sigma weight residual 1.343 1.511 -0.168 1.60e-02 3.91e+03 1.11e+02 bond pdb=" C5' UDP A 603 " pdb=" C4' UDP A 603 " ideal model delta sigma weight residual 1.508 1.397 0.111 1.10e-02 8.26e+03 1.01e+02 bond pdb=" C2 UDP A 603 " pdb=" N3 UDP A 603 " ideal model delta sigma weight residual 1.375 1.517 -0.142 1.70e-02 3.46e+03 7.00e+01 bond pdb=" O3A UDP A 603 " pdb=" PB UDP A 603 " ideal model delta sigma weight residual 1.584 1.659 -0.075 1.00e-02 1.00e+04 5.67e+01 ... (remaining 6198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 8307 2.91 - 5.83: 88 5.83 - 8.74: 14 8.74 - 11.65: 3 11.65 - 14.56: 3 Bond angle restraints: 8415 Sorted by residual: angle pdb=" C2 UDP A 603 " pdb=" N3 UDP A 603 " pdb=" C4 UDP A 603 " ideal model delta sigma weight residual 126.93 120.20 6.73 1.00e+00 1.00e+00 4.54e+01 angle pdb=" O2B UDP A 603 " pdb=" PB UDP A 603 " pdb=" O3A UDP A 603 " ideal model delta sigma weight residual 102.95 109.61 -6.66 1.00e+00 1.00e+00 4.43e+01 angle pdb=" O1B UDP A 603 " pdb=" PB UDP A 603 " pdb=" O3A UDP A 603 " ideal model delta sigma weight residual 102.95 109.42 -6.47 1.00e+00 1.00e+00 4.19e+01 angle pdb=" O5' UDP A 603 " pdb=" PA UDP A 603 " pdb=" O3A UDP A 603 " ideal model delta sigma weight residual 104.35 109.91 -5.56 1.00e+00 1.00e+00 3.09e+01 angle pdb=" N1 UDP A 603 " pdb=" C2 UDP A 603 " pdb=" N3 UDP A 603 " ideal model delta sigma weight residual 114.79 120.18 -5.39 1.00e+00 1.00e+00 2.91e+01 ... (remaining 8410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 3217 16.85 - 33.70: 294 33.70 - 50.55: 50 50.55 - 67.40: 14 67.40 - 84.25: 9 Dihedral angle restraints: 3584 sinusoidal: 1427 harmonic: 2157 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 54.45 38.55 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CB LYS A 314 " pdb=" CG LYS A 314 " pdb=" CD LYS A 314 " pdb=" CE LYS A 314 " ideal model delta sinusoidal sigma weight residual 60.00 116.86 -56.86 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA LYS A 143 " pdb=" CB LYS A 143 " pdb=" CG LYS A 143 " pdb=" CD LYS A 143 " ideal model delta sinusoidal sigma weight residual -180.00 -130.07 -49.93 3 1.50e+01 4.44e-03 8.84e+00 ... (remaining 3581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 841 0.080 - 0.161: 62 0.161 - 0.241: 3 0.241 - 0.322: 2 0.322 - 0.402: 3 Chirality restraints: 911 Sorted by residual: chirality pdb=" CBG Y01 A 602 " pdb=" CAQ Y01 A 602 " pdb=" CBD Y01 A 602 " pdb=" CBI Y01 A 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CBE Y01 A 602 " pdb=" CAP Y01 A 602 " pdb=" CBB Y01 A 602 " pdb=" CBI Y01 A 602 " both_signs ideal model delta sigma weight residual False 2.57 2.92 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CBI Y01 A 602 " pdb=" CAU Y01 A 602 " pdb=" CBE Y01 A 602 " pdb=" CBG Y01 A 602 " both_signs ideal model delta sigma weight residual False 2.94 2.61 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 908 not shown) Planarity restraints: 1034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 270 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO A 271 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 319 " -0.015 5.00e-02 4.00e+02 2.31e-02 8.52e-01 pdb=" N PRO A 320 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 251 " -0.005 2.00e-02 2.50e+03 9.08e-03 8.24e-01 pdb=" C ALA A 251 " 0.016 2.00e-02 2.50e+03 pdb=" O ALA A 251 " -0.006 2.00e-02 2.50e+03 pdb=" N PHE A 252 " -0.005 2.00e-02 2.50e+03 ... (remaining 1031 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 653 2.75 - 3.29: 5636 3.29 - 3.83: 10081 3.83 - 4.36: 11184 4.36 - 4.90: 20097 Nonbonded interactions: 47651 Sorted by model distance: nonbonded pdb=" OD2 ASP B 72 " pdb=" OG1 THR B 74 " model vdw 2.219 3.040 nonbonded pdb=" O3' UDP A 603 " pdb=" O2' UDP A 603 " model vdw 2.367 2.432 nonbonded pdb=" OE1 GLN A 186 " pdb=" NZ LYS A 284 " model vdw 2.391 3.120 nonbonded pdb=" O TRP A 234 " pdb=" OG1 THR A 539 " model vdw 2.397 3.040 nonbonded pdb=" OG SER C 17 " pdb=" O MET C 82 " model vdw 2.401 3.040 ... (remaining 47646 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.370 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 : 0.008 0.230 6205 Z= 0.481 Angle : 0.680 14.565 8419 Z= 0.331 Chirality : 0.047 0.402 911 Planarity : 0.002 0.035 1034 Dihedral : 13.898 84.249 2206 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.32), residues: 732 helix: 2.79 (0.29), residues: 317 sheet: 1.89 (0.44), residues: 142 loop : 0.20 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 39 TYR 0.009 0.001 TYR A 430 PHE 0.007 0.001 PHE A 249 TRP 0.003 0.000 TRP A 502 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.48 ( 6203) covalent geometry : angle 0.68061 / 0.33 ( 8415) SS BOND : bond 0.00129 / 0.07 ( 2) SS BOND : angle 0.38054 / 0.19 ( 4) hydrogen bonds : bond 0.17645 / 11.89 ( 310) hydrogen bonds : angle 5.85320 / 4.26 ( 931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.228 Fit side-chains REVERT: A 372 MET cc_start: 0.7350 (mmt) cc_final: 0.7042 (mmt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0752 time to fit residues: 11.0395 Evaluate side-chains 81 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.157595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127531 restraints weight = 20034.165| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.89 r_work: 0.3476 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6205 Z= 0.103 Angle : 0.443 7.675 8419 Z= 0.235 Chirality : 0.041 0.208 911 Planarity : 0.003 0.034 1034 Dihedral : 6.084 55.604 878 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.32 % Allowed : 6.66 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.32), residues: 732 helix: 2.86 (0.29), residues: 319 sheet: 1.95 (0.42), residues: 155 loop : 0.16 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.019 0.001 TYR A 492 PHE 0.009 0.001 PHE B 47 TRP 0.022 0.001 TRP A 358 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 6203) covalent geometry : angle 0.44311 / 0.24 ( 8415) SS BOND : bond 0.00243 / 0.12 ( 2) SS BOND : angle 0.75587 / 0.28 ( 4) hydrogen bonds : bond 0.03577 / 2.36 ( 310) hydrogen bonds : angle 3.97122 / 2.92 ( 931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 372 MET cc_start: 0.7738 (mmt) cc_final: 0.7379 (mmt) REVERT: B 52 SER cc_start: 0.8927 (m) cc_final: 0.8600 (t) REVERT: B 72 ASP cc_start: 0.6987 (t70) cc_final: 0.6583 (t70) REVERT: B 86 LYS cc_start: 0.7216 (ptpp) cc_final: 0.6874 (ptpp) outliers start: 2 outliers final: 1 residues processed: 89 average time/residue: 0.0676 time to fit residues: 8.3571 Evaluate side-chains 82 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.143644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115136 restraints weight = 13332.469| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.14 r_work: 0.3324 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6205 Z= 0.125 Angle : 0.480 4.886 8419 Z= 0.259 Chirality : 0.042 0.220 911 Planarity : 0.004 0.037 1034 Dihedral : 6.331 57.309 878 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.27 % Allowed : 7.29 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.31), residues: 732 helix: 2.66 (0.29), residues: 320 sheet: 1.62 (0.42), residues: 150 loop : -0.07 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 19 TYR 0.018 0.001 TYR A 492 PHE 0.016 0.001 PHE B 47 TRP 0.020 0.001 TRP A 351 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 6203) covalent geometry : angle 0.47990 / 0.26 ( 8415) SS BOND : bond 0.00175 / 0.09 ( 2) SS BOND : angle 1.15268 / 0.53 ( 4) hydrogen bonds : bond 0.04087 / 2.67 ( 310) hydrogen bonds : angle 3.66675 / 2.72 ( 931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.137 Fit side-chains REVERT: A 372 MET cc_start: 0.7855 (mmt) cc_final: 0.7514 (mmt) REVERT: B 52 SER cc_start: 0.9046 (m) cc_final: 0.8719 (t) REVERT: C 60 TYR cc_start: 0.7895 (t80) cc_final: 0.7685 (t80) REVERT: C 75 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8248 (mtm-85) outliers start: 8 outliers final: 6 residues processed: 85 average time/residue: 0.0640 time to fit residues: 7.4506 Evaluate side-chains 79 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 68 optimal weight: 0.0070 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112190 restraints weight = 20936.795| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.92 r_work: 0.3265 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6205 Z= 0.108 Angle : 0.437 7.016 8419 Z= 0.236 Chirality : 0.041 0.216 911 Planarity : 0.003 0.034 1034 Dihedral : 6.360 57.830 878 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.27 % Allowed : 9.19 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.31), residues: 732 helix: 2.68 (0.29), residues: 320 sheet: 1.54 (0.42), residues: 149 loop : -0.27 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 75 TYR 0.015 0.001 TYR A 492 PHE 0.010 0.001 PHE B 47 TRP 0.017 0.001 TRP A 351 HIS 0.001 0.000 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 6203) covalent geometry : angle 0.43718 / 0.24 ( 8415) SS BOND : bond 0.00235 / 0.12 ( 2) SS BOND : angle 0.64699 / 0.30 ( 4) hydrogen bonds : bond 0.03674 / 2.40 ( 310) hydrogen bonds : angle 3.55460 / 2.66 ( 931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.219 Fit side-chains REVERT: A 372 MET cc_start: 0.7803 (mmt) cc_final: 0.7487 (mmt) REVERT: B 52 SER cc_start: 0.9048 (m) cc_final: 0.8788 (t) REVERT: C 60 TYR cc_start: 0.7974 (t80) cc_final: 0.7762 (t80) outliers start: 8 outliers final: 8 residues processed: 80 average time/residue: 0.0651 time to fit residues: 7.3163 Evaluate side-chains 79 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.142124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112609 restraints weight = 16969.321| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.54 r_work: 0.3280 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6205 Z= 0.103 Angle : 0.428 5.937 8419 Z= 0.232 Chirality : 0.041 0.208 911 Planarity : 0.003 0.036 1034 Dihedral : 6.432 59.752 878 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.43 % Allowed : 10.14 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.31), residues: 732 helix: 2.71 (0.29), residues: 319 sheet: 1.20 (0.40), residues: 160 loop : -0.33 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.015 0.001 TYR A 492 PHE 0.010 0.001 PHE B 47 TRP 0.020 0.001 TRP A 351 HIS 0.001 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 6203) covalent geometry : angle 0.42803 / 0.23 ( 8415) SS BOND : bond 0.00252 / 0.13 ( 2) SS BOND : angle 0.73010 / 0.35 ( 4) hydrogen bonds : bond 0.03633 / 2.37 ( 310) hydrogen bonds : angle 3.49341 / 2.63 ( 931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.228 Fit side-chains REVERT: A 333 MET cc_start: 0.8219 (mmm) cc_final: 0.8011 (mmt) REVERT: A 372 MET cc_start: 0.7720 (mmt) cc_final: 0.7411 (mmt) REVERT: B 52 SER cc_start: 0.9081 (m) cc_final: 0.8817 (t) outliers start: 9 outliers final: 9 residues processed: 77 average time/residue: 0.0704 time to fit residues: 7.4519 Evaluate side-chains 78 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109400 restraints weight = 13420.618| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.07 r_work: 0.3255 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6205 Z= 0.139 Angle : 0.478 5.381 8419 Z= 0.258 Chirality : 0.042 0.207 911 Planarity : 0.003 0.041 1034 Dihedral : 6.658 58.181 878 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.58 % Allowed : 10.30 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.31), residues: 732 helix: 2.48 (0.29), residues: 325 sheet: 1.04 (0.40), residues: 160 loop : -0.40 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 19 TYR 0.014 0.001 TYR A 430 PHE 0.013 0.001 PHE B 47 TRP 0.022 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 6203) covalent geometry : angle 0.47784 / 0.26 ( 8415) SS BOND : bond 0.00191 / 0.09 ( 2) SS BOND : angle 0.92826 / 0.43 ( 4) hydrogen bonds : bond 0.04212 / 2.76 ( 310) hydrogen bonds : angle 3.60946 / 2.72 ( 931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.204 Fit side-chains REVERT: A 372 MET cc_start: 0.7793 (mmt) cc_final: 0.7593 (mmt) REVERT: B 52 SER cc_start: 0.9106 (m) cc_final: 0.8831 (t) outliers start: 10 outliers final: 9 residues processed: 79 average time/residue: 0.0690 time to fit residues: 7.6339 Evaluate side-chains 72 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.136484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107402 restraints weight = 19354.384| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.65 r_work: 0.3211 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6205 Z= 0.135 Angle : 0.464 5.652 8419 Z= 0.251 Chirality : 0.041 0.187 911 Planarity : 0.003 0.037 1034 Dihedral : 6.592 58.663 878 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.58 % Allowed : 11.09 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.31), residues: 732 helix: 2.43 (0.29), residues: 325 sheet: 0.98 (0.39), residues: 161 loop : -0.40 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 19 TYR 0.015 0.001 TYR A 492 PHE 0.012 0.001 PHE B 47 TRP 0.023 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6203) covalent geometry : angle 0.46329 / 0.25 ( 8415) SS BOND : bond 0.00227 / 0.11 ( 2) SS BOND : angle 0.83043 / 0.39 ( 4) hydrogen bonds : bond 0.04105 / 2.70 ( 310) hydrogen bonds : angle 3.60106 / 2.70 ( 931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.136 Fit side-chains REVERT: B 52 SER cc_start: 0.9124 (m) cc_final: 0.8885 (t) REVERT: B 64 LYS cc_start: 0.6546 (mmmt) cc_final: 0.6299 (mmtt) REVERT: C 19 ARG cc_start: 0.7917 (ttt90) cc_final: 0.7612 (tpt-90) outliers start: 10 outliers final: 10 residues processed: 74 average time/residue: 0.0645 time to fit residues: 6.5962 Evaluate side-chains 77 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 0.0020 chunk 52 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.108083 restraints weight = 20908.802| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.79 r_work: 0.3207 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6205 Z= 0.113 Angle : 0.438 5.777 8419 Z= 0.238 Chirality : 0.040 0.173 911 Planarity : 0.003 0.038 1034 Dihedral : 6.521 58.993 878 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.74 % Allowed : 11.25 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.31), residues: 732 helix: 2.49 (0.29), residues: 326 sheet: 0.96 (0.40), residues: 161 loop : -0.36 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.018 0.001 TYR C 106 PHE 0.010 0.001 PHE B 47 TRP 0.018 0.001 TRP A 351 HIS 0.001 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 6203) covalent geometry : angle 0.43773 / 0.24 ( 8415) SS BOND : bond 0.00246 / 0.12 ( 2) SS BOND : angle 0.80238 / 0.36 ( 4) hydrogen bonds : bond 0.03845 / 2.53 ( 310) hydrogen bonds : angle 3.53851 / 2.64 ( 931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.218 Fit side-chains REVERT: A 301 ASP cc_start: 0.6446 (m-30) cc_final: 0.6051 (m-30) REVERT: B 52 SER cc_start: 0.9110 (m) cc_final: 0.8888 (t) REVERT: B 64 LYS cc_start: 0.6772 (mmmt) cc_final: 0.6534 (mmtt) outliers start: 11 outliers final: 11 residues processed: 78 average time/residue: 0.0628 time to fit residues: 6.7029 Evaluate side-chains 76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107594 restraints weight = 13775.147| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.04 r_work: 0.3229 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6205 Z= 0.149 Angle : 0.479 6.024 8419 Z= 0.258 Chirality : 0.042 0.169 911 Planarity : 0.003 0.037 1034 Dihedral : 6.742 59.618 878 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.58 % Allowed : 11.89 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.31), residues: 732 helix: 2.37 (0.29), residues: 327 sheet: 0.91 (0.40), residues: 161 loop : -0.38 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 71 TYR 0.016 0.001 TYR C 106 PHE 0.014 0.001 PHE B 47 TRP 0.017 0.001 TRP A 351 HIS 0.002 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 6203) covalent geometry : angle 0.47848 / 0.26 ( 8415) SS BOND : bond 0.00253 / 0.12 ( 2) SS BOND : angle 0.95665 / 0.45 ( 4) hydrogen bonds : bond 0.04320 / 2.84 ( 310) hydrogen bonds : angle 3.65099 / 2.73 ( 931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.215 Fit side-chains REVERT: A 301 ASP cc_start: 0.6261 (m-30) cc_final: 0.5891 (m-30) REVERT: B 52 SER cc_start: 0.9129 (m) cc_final: 0.8910 (t) REVERT: B 64 LYS cc_start: 0.6830 (mmmt) cc_final: 0.6607 (mmtt) outliers start: 10 outliers final: 10 residues processed: 74 average time/residue: 0.0774 time to fit residues: 7.7509 Evaluate side-chains 74 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108025 restraints weight = 23340.115| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.98 r_work: 0.3204 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6205 Z= 0.099 Angle : 0.424 6.229 8419 Z= 0.232 Chirality : 0.040 0.162 911 Planarity : 0.003 0.039 1034 Dihedral : 6.482 59.342 878 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.90 % Allowed : 11.41 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.31), residues: 732 helix: 2.50 (0.29), residues: 327 sheet: 0.95 (0.40), residues: 161 loop : -0.30 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 334 TYR 0.016 0.001 TYR C 106 PHE 0.008 0.001 PHE A 49 TRP 0.017 0.001 TRP A 351 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 6203) covalent geometry : angle 0.42407 / 0.23 ( 8415) SS BOND : bond 0.00290 / 0.14 ( 2) SS BOND : angle 0.73960 / 0.32 ( 4) hydrogen bonds : bond 0.03727 / 2.46 ( 310) hydrogen bonds : angle 3.55420 / 2.64 ( 931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.189 Fit side-chains REVERT: A 301 ASP cc_start: 0.6253 (m-30) cc_final: 0.5884 (m-30) REVERT: B 52 SER cc_start: 0.9164 (m) cc_final: 0.8921 (t) outliers start: 12 outliers final: 10 residues processed: 78 average time/residue: 0.0691 time to fit residues: 7.5580 Evaluate side-chains 77 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 0.0070 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 9 optimal weight: 0.0370 chunk 64 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.1654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.113534 restraints weight = 17113.952| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.46 r_work: 0.3289 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6205 Z= 0.084 Angle : 0.406 6.094 8419 Z= 0.220 Chirality : 0.039 0.158 911 Planarity : 0.003 0.040 1034 Dihedral : 6.139 58.387 878 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.43 % Allowed : 12.20 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.31), residues: 732 helix: 2.74 (0.29), residues: 321 sheet: 1.09 (0.40), residues: 160 loop : -0.17 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 334 TYR 0.016 0.001 TYR C 106 PHE 0.008 0.001 PHE A 53 TRP 0.032 0.001 TRP A 351 HIS 0.000 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00169 / 0.08 ( 6203) covalent geometry : angle 0.40626 / 0.22 ( 8415) SS BOND : bond 0.00328 / 0.16 ( 2) SS BOND : angle 0.70323 / 0.30 ( 4) hydrogen bonds : bond 0.03241 / 2.13 ( 310) hydrogen bonds : angle 3.46647 / 2.55 ( 931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1586.69 seconds wall clock time: 27 minutes 47.39 seconds (1667.39 seconds total)