Starting phenix.real_space_refine on Wed Jun 3 13:15:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iaz_52787/06_2026/9iaz_52787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iaz_52787/06_2026/9iaz_52787.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9iaz_52787/06_2026/9iaz_52787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iaz_52787/06_2026/9iaz_52787.map" model { file = "/net/cci-nas-00/data/ceres_data/9iaz_52787/06_2026/9iaz_52787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iaz_52787/06_2026/9iaz_52787.cif" } 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 25 5.16 5 C 3618 2.51 5 N 950 2.21 5 O 1064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5657 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 490 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "B" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4268 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 899 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Time building chain proxies: 1.44, per 1000 atoms: 0.25 Number of scatterers: 5657 At special positions: 0 Unit cell: (69.46, 110.23, 101.925, 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 25 16.00 O 1064 8.00 N 950 7.00 C 3618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 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: 0.41 Conformation dependent library (CDL) restraints added in 348.9 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 12 sheets defined 8.9% alpha, 45.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.768A pdb=" N LEU B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 191 removed outlier: 3.556A pdb=" N ILE B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.687A pdb=" N ALA B 475 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 476 " --> pdb=" O LEU B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 476' Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.935A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 206 removed outlier: 6.660A pdb=" N LYS A 195 " --> pdb=" O MET A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.541A pdb=" N LYS B 50 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 234 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLN B 232 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 54 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B 230 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL B 56 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL B 228 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LYS B 58 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS B 226 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 60 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE B 224 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU B 62 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR B 222 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.792A pdb=" N LEU B 85 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR B 199 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR B 222 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU B 62 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE B 224 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 60 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS B 226 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LYS B 58 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL B 228 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL B 56 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B 230 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 54 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLN B 232 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 234 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 50 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU B 251 " --> pdb=" O GLN B 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 164 removed outlier: 6.134A pdb=" N GLU B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU B 143 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET B 149 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL B 141 " --> pdb=" O MET B 149 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER B 151 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA6, first strand: chain 'B' and resid 457 through 459 removed outlier: 5.446A pdb=" N LEU B 481 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B 321 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 483 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS B 311 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER B 493 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE B 309 " --> pdb=" O SER B 493 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 306 through 322 current: chain 'B' and resid 528 through 529 Processing sheet with id=AA7, first strand: chain 'B' and resid 512 through 518 removed outlier: 7.006A pdb=" N THR B 512 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 284 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE B 309 " --> pdb=" O SER B 493 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER B 493 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS B 311 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 483 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B 321 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU B 481 " --> pdb=" O SER B 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 479 through 494 current: chain 'B' and resid 533 through 535 Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 351 removed outlier: 3.638A pdb=" N THR B 351 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY B 432 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 365 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN B 388 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 416 " --> pdb=" O GLN B 388 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 397 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 410 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU B 395 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 351 removed outlier: 3.638A pdb=" N THR B 351 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY B 432 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 365 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN B 388 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 416 " --> pdb=" O GLN B 388 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.298A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.298A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR C 107 " --> pdb=" O ALA C 98 " (cutoff:3.500A) 162 hydrogen bonds defined for protein. 429 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: 0.57 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: 1841 1.34 - 1.46: 1274 1.46 - 1.58: 2635 1.58 - 1.70: 0 1.70 - 1.81: 40 Bond restraints: 5790 Sorted by residual: bond pdb=" N ILE B 318 " pdb=" CA ILE B 318 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.19e-02 7.06e+03 9.47e+00 bond pdb=" N ILE B 357 " pdb=" CA ILE B 357 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.30e-02 5.92e+03 9.46e+00 bond pdb=" N VAL B 154 " pdb=" CA VAL B 154 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.11e-02 8.12e+03 8.29e+00 bond pdb=" N ILE B 438 " pdb=" CA ILE B 438 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 8.01e+00 bond pdb=" CA SER B 337 " pdb=" CB SER B 337 " ideal model delta sigma weight residual 1.530 1.488 0.042 1.51e-02 4.39e+03 7.87e+00 ... (remaining 5785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 7386 1.03 - 2.06: 340 2.06 - 3.09: 97 3.09 - 4.11: 18 4.11 - 5.14: 4 Bond angle restraints: 7845 Sorted by residual: angle pdb=" CA GLY B 478 " pdb=" C GLY B 478 " pdb=" N LEU B 479 " ideal model delta sigma weight residual 114.58 117.46 -2.88 8.60e-01 1.35e+00 1.12e+01 angle pdb=" CA VAL B 154 " pdb=" C VAL B 154 " pdb=" O VAL B 154 " ideal model delta sigma weight residual 121.67 118.18 3.49 1.05e+00 9.07e-01 1.11e+01 angle pdb=" CA ARG B 317 " pdb=" C ARG B 317 " pdb=" O ARG B 317 " ideal model delta sigma weight residual 121.44 117.59 3.85 1.17e+00 7.31e-01 1.08e+01 angle pdb=" N VAL B 506 " pdb=" CA VAL B 506 " pdb=" C VAL B 506 " ideal model delta sigma weight residual 113.42 109.71 3.71 1.17e+00 7.31e-01 1.01e+01 angle pdb=" CA HIS B 106 " pdb=" CB HIS B 106 " pdb=" CG HIS B 106 " ideal model delta sigma weight residual 113.80 116.85 -3.05 1.00e+00 1.00e+00 9.33e+00 ... (remaining 7840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 2963 16.72 - 33.45: 398 33.45 - 50.17: 103 50.17 - 66.89: 34 66.89 - 83.62: 6 Dihedral angle restraints: 3504 sinusoidal: 1447 harmonic: 2057 Sorted by residual: dihedral pdb=" CG ARG B 544 " pdb=" CD ARG B 544 " pdb=" NE ARG B 544 " pdb=" CZ ARG B 544 " ideal model delta sinusoidal sigma weight residual -90.00 -133.74 43.74 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG B 156 " pdb=" CD ARG B 156 " pdb=" NE ARG B 156 " pdb=" CZ ARG B 156 " ideal model delta sinusoidal sigma weight residual 180.00 137.91 42.09 2 1.50e+01 4.44e-03 9.58e+00 dihedral pdb=" CA TYR B 444 " pdb=" C TYR B 444 " pdb=" N PRO B 445 " pdb=" CA PRO B 445 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.51e+00 ... (remaining 3501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 677 0.044 - 0.088: 120 0.088 - 0.132: 59 0.132 - 0.176: 7 0.176 - 0.220: 2 Chirality restraints: 865 Sorted by residual: chirality pdb=" CA VAL B 188 " pdb=" N VAL B 188 " pdb=" C VAL B 188 " pdb=" CB VAL B 188 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL B 308 " pdb=" CA VAL B 308 " pdb=" CG1 VAL B 308 " pdb=" CG2 VAL B 308 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ARG B 317 " pdb=" N ARG B 317 " pdb=" C ARG B 317 " pdb=" CB ARG B 317 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 862 not shown) Planarity restraints: 1013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 317 " 0.244 9.50e-02 1.11e+02 1.09e-01 7.34e+00 pdb=" NE ARG B 317 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 317 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 317 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 317 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 187 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C ILE B 187 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE B 187 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 188 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 497 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO B 498 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 498 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 498 " -0.019 5.00e-02 4.00e+02 ... (remaining 1010 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 824 2.77 - 3.30: 4688 3.30 - 3.83: 8245 3.83 - 4.37: 9640 4.37 - 4.90: 17853 Nonbonded interactions: 41250 Sorted by model distance: nonbonded pdb=" OD2 ASP B 440 " pdb=" OH TYR B 444 " model vdw 2.232 3.040 nonbonded pdb=" OD2 ASP B 178 " pdb=" OH TYR B 182 " model vdw 2.238 3.040 nonbonded pdb=" OD1 ASP B 487 " pdb=" OH TYR B 546 " model vdw 2.283 3.040 nonbonded pdb=" OG SER B 4 " pdb=" OE1 GLU B 7 " model vdw 2.284 3.040 nonbonded pdb=" N GLU B 177 " pdb=" OE1 GLU B 177 " model vdw 2.346 3.120 ... (remaining 41245 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.050 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 0.045 5791 Z= 0.182 Angle : 0.557 5.144 7847 Z= 0.336 Chirality : 0.045 0.220 865 Planarity : 0.005 0.109 1013 Dihedral : 16.861 83.617 2169 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.64 % Allowed : 25.76 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.31), residues: 690 helix: -2.42 (0.68), residues: 51 sheet: 0.05 (0.35), residues: 234 loop : -0.83 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.019 0.001 TYR B 546 PHE 0.006 0.001 PHE B 332 TRP 0.014 0.001 TRP C 36 HIS 0.005 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.18 ( 5790) covalent geometry : angle 0.55731 / 0.34 ( 7845) SS BOND : bond 0.00770 / 0.51 ( 1) SS BOND : angle 0.50492 / 0.33 ( 2) hydrogen bonds : bond 0.17243 / 11.32 ( 140) hydrogen bonds : angle 7.65808 / 5.32 ( 429) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: B 22 GLU cc_start: 0.7071 (pp20) cc_final: 0.6754 (pp20) REVERT: B 55 LYS cc_start: 0.7790 (ttpt) cc_final: 0.7503 (mmtm) REVERT: B 371 LYS cc_start: 0.8159 (tttm) cc_final: 0.7810 (mtmm) REVERT: B 538 GLU cc_start: 0.8435 (tt0) cc_final: 0.8228 (tt0) outliers start: 4 outliers final: 3 residues processed: 71 average time/residue: 0.0997 time to fit residues: 8.9028 Evaluate side-chains 67 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.0370 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.0870 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.166607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125577 restraints weight = 6476.507| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.77 r_work: 0.3135 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5791 Z= 0.104 Angle : 0.478 4.480 7847 Z= 0.252 Chirality : 0.042 0.137 865 Planarity : 0.003 0.030 1013 Dihedral : 4.210 37.795 764 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.70 % Allowed : 22.73 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.72 (0.31), residues: 690 helix: -2.13 (0.68), residues: 50 sheet: 0.27 (0.35), residues: 242 loop : -0.70 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 508 TYR 0.007 0.001 TYR B 182 PHE 0.009 0.001 PHE B 8 TRP 0.005 0.001 TRP B 263 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.10 ( 5790) covalent geometry : angle 0.47807 / 0.25 ( 7845) SS BOND : bond 0.00554 / 0.37 ( 1) SS BOND : angle 0.13111 / 0.08 ( 2) hydrogen bonds : bond 0.03526 / 2.38 ( 140) hydrogen bonds : angle 5.35518 / 3.67 ( 429) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: B 22 GLU cc_start: 0.6834 (pp20) cc_final: 0.6136 (pp20) REVERT: B 24 GLN cc_start: 0.6901 (mm110) cc_final: 0.6501 (mm110) REVERT: B 55 LYS cc_start: 0.7751 (ttpt) cc_final: 0.7420 (mmtm) REVERT: B 128 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5383 (tp) REVERT: B 137 MET cc_start: 0.7817 (ttt) cc_final: 0.7521 (ttm) REVERT: B 371 LYS cc_start: 0.8171 (tttm) cc_final: 0.7813 (mtmm) outliers start: 17 outliers final: 11 residues processed: 83 average time/residue: 0.0828 time to fit residues: 8.8973 Evaluate side-chains 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 0.0070 chunk 43 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.166781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126594 restraints weight = 6438.577| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.54 r_work: 0.3150 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5791 Z= 0.100 Angle : 0.455 4.495 7847 Z= 0.239 Chirality : 0.042 0.137 865 Planarity : 0.003 0.028 1013 Dihedral : 3.932 23.453 763 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.66 % Allowed : 21.62 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.72 (0.31), residues: 690 helix: -1.64 (0.71), residues: 50 sheet: 0.27 (0.35), residues: 242 loop : -0.78 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 544 TYR 0.014 0.001 TYR B 95 PHE 0.007 0.001 PHE B 86 TRP 0.005 0.001 TRP B 263 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 ( 5790) covalent geometry : angle 0.45498 / 0.24 ( 7845) SS BOND : bond 0.00532 / 0.35 ( 1) SS BOND : angle 0.16056 / 0.09 ( 2) hydrogen bonds : bond 0.03283 / 2.18 ( 140) hydrogen bonds : angle 4.88326 / 3.36 ( 429) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: B 22 GLU cc_start: 0.6978 (pp20) cc_final: 0.6335 (pp20) REVERT: B 24 GLN cc_start: 0.6767 (mm110) cc_final: 0.6507 (mm110) REVERT: B 55 LYS cc_start: 0.7730 (ttpt) cc_final: 0.7395 (mmtm) REVERT: B 137 MET cc_start: 0.7975 (ttt) cc_final: 0.7704 (ttm) REVERT: B 371 LYS cc_start: 0.8121 (tttm) cc_final: 0.7760 (mtmm) outliers start: 23 outliers final: 14 residues processed: 84 average time/residue: 0.0759 time to fit residues: 8.4718 Evaluate side-chains 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 25 optimal weight: 0.0050 overall best weight: 0.3952 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.167390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126786 restraints weight = 6476.326| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.59 r_work: 0.3149 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5791 Z= 0.096 Angle : 0.459 5.790 7847 Z= 0.239 Chirality : 0.041 0.139 865 Planarity : 0.003 0.027 1013 Dihedral : 3.875 23.275 763 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.02 % Allowed : 22.26 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.63 (0.31), residues: 690 helix: -1.41 (0.73), residues: 50 sheet: 0.32 (0.35), residues: 237 loop : -0.72 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 544 TYR 0.009 0.001 TYR B 118 PHE 0.010 0.001 PHE B 163 TRP 0.007 0.001 TRP C 36 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 5790) covalent geometry : angle 0.45899 / 0.24 ( 7845) SS BOND : bond 0.00581 / 0.39 ( 1) SS BOND : angle 0.26733 / 0.18 ( 2) hydrogen bonds : bond 0.03155 / 2.08 ( 140) hydrogen bonds : angle 4.70337 / 3.24 ( 429) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: B 20 VAL cc_start: 0.8908 (t) cc_final: 0.8686 (p) REVERT: B 22 GLU cc_start: 0.7021 (pp20) cc_final: 0.6412 (pp20) REVERT: B 55 LYS cc_start: 0.7676 (ttpt) cc_final: 0.7320 (mmtm) REVERT: B 137 MET cc_start: 0.7906 (ttt) cc_final: 0.7614 (ttm) REVERT: B 371 LYS cc_start: 0.8124 (tttm) cc_final: 0.7725 (mtmm) outliers start: 19 outliers final: 15 residues processed: 77 average time/residue: 0.0728 time to fit residues: 7.5835 Evaluate side-chains 77 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.165560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124038 restraints weight = 6628.978| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.79 r_work: 0.3120 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5791 Z= 0.129 Angle : 0.483 5.170 7847 Z= 0.253 Chirality : 0.043 0.140 865 Planarity : 0.003 0.031 1013 Dihedral : 4.076 23.959 763 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.29 % Allowed : 21.94 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.73 (0.31), residues: 690 helix: -1.32 (0.74), residues: 50 sheet: 0.21 (0.35), residues: 234 loop : -0.77 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 544 TYR 0.011 0.001 TYR B 95 PHE 0.010 0.001 PHE C 47 TRP 0.005 0.001 TRP B 263 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 ( 5790) covalent geometry : angle 0.48254 / 0.25 ( 7845) SS BOND : bond 0.00526 / 0.35 ( 1) SS BOND : angle 0.36982 / 0.20 ( 2) hydrogen bonds : bond 0.03345 / 2.20 ( 140) hydrogen bonds : angle 4.79196 / 3.28 ( 429) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: B 20 VAL cc_start: 0.8959 (t) cc_final: 0.8689 (p) REVERT: B 22 GLU cc_start: 0.7164 (pp20) cc_final: 0.6742 (pp20) REVERT: B 55 LYS cc_start: 0.7673 (ttpt) cc_final: 0.7292 (mmtm) REVERT: B 137 MET cc_start: 0.7946 (ttt) cc_final: 0.7643 (ttm) REVERT: B 245 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8675 (mp) REVERT: B 371 LYS cc_start: 0.8231 (tttm) cc_final: 0.7809 (mtmm) REVERT: C 38 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8856 (ptt180) outliers start: 27 outliers final: 20 residues processed: 86 average time/residue: 0.0683 time to fit residues: 7.9806 Evaluate side-chains 83 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.0670 chunk 59 optimal weight: 0.8980 chunk 66 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 0.0370 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.166786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126988 restraints weight = 6483.349| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.71 r_work: 0.3146 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5791 Z= 0.086 Angle : 0.448 4.489 7847 Z= 0.236 Chirality : 0.041 0.137 865 Planarity : 0.003 0.028 1013 Dihedral : 3.886 22.822 763 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.70 % Allowed : 23.85 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.61 (0.31), residues: 690 helix: -1.24 (0.74), residues: 50 sheet: 0.32 (0.35), residues: 228 loop : -0.70 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.008 0.001 TYR B 118 PHE 0.007 0.001 PHE B 86 TRP 0.008 0.001 TRP C 36 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 ( 5790) covalent geometry : angle 0.44816 / 0.24 ( 7845) SS BOND : bond 0.00556 / 0.37 ( 1) SS BOND : angle 0.21295 / 0.15 ( 2) hydrogen bonds : bond 0.02886 / 1.89 ( 140) hydrogen bonds : angle 4.53546 / 3.12 ( 429) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: B 20 VAL cc_start: 0.8921 (t) cc_final: 0.8690 (p) REVERT: B 22 GLU cc_start: 0.7168 (pp20) cc_final: 0.6865 (pp20) REVERT: B 55 LYS cc_start: 0.7708 (ttpt) cc_final: 0.7411 (mmtm) REVERT: B 137 MET cc_start: 0.7936 (ttt) cc_final: 0.7653 (ttm) REVERT: B 243 ARG cc_start: 0.8669 (mtt90) cc_final: 0.8416 (mtt90) REVERT: B 371 LYS cc_start: 0.8166 (tttm) cc_final: 0.7820 (mtmm) outliers start: 17 outliers final: 14 residues processed: 76 average time/residue: 0.0894 time to fit residues: 8.7405 Evaluate side-chains 73 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 chunk 6 optimal weight: 0.0370 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.168125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128654 restraints weight = 6651.457| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.62 r_work: 0.3166 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5791 Z= 0.077 Angle : 0.430 4.140 7847 Z= 0.226 Chirality : 0.041 0.137 865 Planarity : 0.003 0.027 1013 Dihedral : 3.749 22.374 763 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.70 % Allowed : 23.53 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.68 (0.31), residues: 690 helix: -1.05 (0.75), residues: 50 sheet: 0.30 (0.36), residues: 215 loop : -0.77 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 243 TYR 0.008 0.001 TYR B 353 PHE 0.006 0.001 PHE B 373 TRP 0.005 0.001 TRP B 502 HIS 0.003 0.000 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.08 ( 5790) covalent geometry : angle 0.43034 / 0.23 ( 7845) SS BOND : bond 0.00502 / 0.33 ( 1) SS BOND : angle 0.26104 / 0.16 ( 2) hydrogen bonds : bond 0.02653 / 1.73 ( 140) hydrogen bonds : angle 4.39182 / 3.02 ( 429) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: B 22 GLU cc_start: 0.7193 (pp20) cc_final: 0.6858 (pp20) REVERT: B 55 LYS cc_start: 0.7687 (ttpt) cc_final: 0.7414 (mmtm) REVERT: B 137 MET cc_start: 0.7930 (ttt) cc_final: 0.7657 (ttm) REVERT: B 243 ARG cc_start: 0.8651 (mtt90) cc_final: 0.8405 (mtt90) REVERT: B 371 LYS cc_start: 0.8122 (tttm) cc_final: 0.7796 (mtmm) outliers start: 17 outliers final: 14 residues processed: 77 average time/residue: 0.0783 time to fit residues: 7.7930 Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 49 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 66 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.166905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128094 restraints weight = 6484.847| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.42 r_work: 0.3167 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5791 Z= 0.103 Angle : 0.452 4.987 7847 Z= 0.238 Chirality : 0.042 0.136 865 Planarity : 0.003 0.027 1013 Dihedral : 3.774 22.826 761 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.82 % Allowed : 22.73 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.63 (0.31), residues: 690 helix: -1.06 (0.75), residues: 50 sheet: 0.28 (0.35), residues: 232 loop : -0.73 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 544 TYR 0.010 0.001 TYR B 118 PHE 0.009 0.001 PHE B 163 TRP 0.004 0.001 TRP B 263 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.10 ( 5790) covalent geometry : angle 0.45204 / 0.24 ( 7845) SS BOND : bond 0.00527 / 0.35 ( 1) SS BOND : angle 0.28401 / 0.16 ( 2) hydrogen bonds : bond 0.02883 / 1.89 ( 140) hydrogen bonds : angle 4.45536 / 3.06 ( 429) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: B 20 VAL cc_start: 0.8952 (t) cc_final: 0.8731 (p) REVERT: B 22 GLU cc_start: 0.7189 (pp20) cc_final: 0.6872 (pp20) REVERT: B 55 LYS cc_start: 0.7691 (ttpt) cc_final: 0.7426 (mmtm) REVERT: B 137 MET cc_start: 0.7930 (ttt) cc_final: 0.7656 (ttm) REVERT: B 163 PHE cc_start: 0.4668 (OUTLIER) cc_final: 0.4132 (p90) REVERT: B 245 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8674 (mp) REVERT: B 371 LYS cc_start: 0.8110 (tttm) cc_final: 0.7801 (mtmm) outliers start: 24 outliers final: 19 residues processed: 77 average time/residue: 0.0623 time to fit residues: 6.6049 Evaluate side-chains 80 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.4916 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.166273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127770 restraints weight = 6621.972| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.67 r_work: 0.3145 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5791 Z= 0.105 Angle : 0.460 4.857 7847 Z= 0.243 Chirality : 0.042 0.137 865 Planarity : 0.003 0.027 1013 Dihedral : 3.864 23.088 761 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.50 % Allowed : 23.05 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.69 (0.31), residues: 690 helix: -1.08 (0.74), residues: 50 sheet: 0.23 (0.35), residues: 229 loop : -0.76 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 38 TYR 0.009 0.001 TYR B 118 PHE 0.008 0.001 PHE C 47 TRP 0.004 0.001 TRP B 263 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.10 ( 5790) covalent geometry : angle 0.46047 / 0.24 ( 7845) SS BOND : bond 0.00457 / 0.30 ( 1) SS BOND : angle 0.39681 / 0.24 ( 2) hydrogen bonds : bond 0.02974 / 1.95 ( 140) hydrogen bonds : angle 4.50877 / 3.09 ( 429) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: B 20 VAL cc_start: 0.8978 (t) cc_final: 0.8763 (p) REVERT: B 22 GLU cc_start: 0.7204 (pp20) cc_final: 0.6860 (pp20) REVERT: B 55 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7380 (mmtm) REVERT: B 137 MET cc_start: 0.7963 (ttt) cc_final: 0.7691 (ttm) REVERT: B 163 PHE cc_start: 0.4719 (OUTLIER) cc_final: 0.4104 (p90) REVERT: B 245 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8680 (mp) REVERT: B 371 LYS cc_start: 0.8117 (tttm) cc_final: 0.7813 (mtmm) outliers start: 22 outliers final: 20 residues processed: 78 average time/residue: 0.0754 time to fit residues: 7.8506 Evaluate side-chains 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.165664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127235 restraints weight = 6677.429| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.62 r_work: 0.3129 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5791 Z= 0.112 Angle : 0.470 4.863 7847 Z= 0.246 Chirality : 0.042 0.137 865 Planarity : 0.003 0.028 1013 Dihedral : 3.917 23.100 761 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.34 % Allowed : 23.37 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.64 (0.31), residues: 690 helix: -1.12 (0.74), residues: 50 sheet: 0.30 (0.35), residues: 231 loop : -0.75 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 544 TYR 0.010 0.001 TYR B 118 PHE 0.008 0.001 PHE C 47 TRP 0.005 0.001 TRP B 263 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.11 ( 5790) covalent geometry : angle 0.47012 / 0.25 ( 7845) SS BOND : bond 0.00491 / 0.33 ( 1) SS BOND : angle 0.36215 / 0.22 ( 2) hydrogen bonds : bond 0.03055 / 2.01 ( 140) hydrogen bonds : angle 4.55678 / 3.13 ( 429) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: B 20 VAL cc_start: 0.8984 (t) cc_final: 0.8772 (p) REVERT: B 22 GLU cc_start: 0.7183 (pp20) cc_final: 0.6829 (pp20) REVERT: B 55 LYS cc_start: 0.7713 (ttpt) cc_final: 0.7384 (mmtm) REVERT: B 137 MET cc_start: 0.7974 (ttt) cc_final: 0.7704 (ttm) REVERT: B 245 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8718 (mp) REVERT: B 371 LYS cc_start: 0.8144 (tttm) cc_final: 0.7865 (mtmm) outliers start: 21 outliers final: 20 residues processed: 74 average time/residue: 0.0857 time to fit residues: 8.2807 Evaluate side-chains 76 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 44 optimal weight: 0.7980 chunk 50 optimal weight: 0.0970 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 0.0000 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 overall best weight: 0.4582 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.166240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127848 restraints weight = 6547.124| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.59 r_work: 0.3149 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5791 Z= 0.102 Angle : 0.459 4.713 7847 Z= 0.241 Chirality : 0.042 0.136 865 Planarity : 0.003 0.028 1013 Dihedral : 3.889 22.719 761 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.50 % Allowed : 23.21 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.64 (0.31), residues: 690 helix: -1.03 (0.75), residues: 50 sheet: 0.31 (0.36), residues: 221 loop : -0.75 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 544 TYR 0.010 0.001 TYR B 118 PHE 0.008 0.001 PHE B 86 TRP 0.004 0.001 TRP B 263 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.10 ( 5790) covalent geometry : angle 0.45877 / 0.24 ( 7845) SS BOND : bond 0.00464 / 0.31 ( 1) SS BOND : angle 0.35807 / 0.22 ( 2) hydrogen bonds : bond 0.02936 / 1.93 ( 140) hydrogen bonds : angle 4.48989 / 3.09 ( 429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1543.35 seconds wall clock time: 27 minutes 11.01 seconds (1631.01 seconds total)