Starting phenix.real_space_refine on Sat Apr 4 23:10:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k0o_61949/04_2026/9k0o_61949.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k0o_61949/04_2026/9k0o_61949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k0o_61949/04_2026/9k0o_61949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k0o_61949/04_2026/9k0o_61949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k0o_61949/04_2026/9k0o_61949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k0o_61949/04_2026/9k0o_61949.map" } resolution = 2.95 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= -0.003 sd= 0.093 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 Cl 1 4.86 5 C 3658 2.51 5 N 870 2.21 5 O 967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5534 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 854 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "L" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 732 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 3939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3939 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 27, 'TRANS': 493} Chain breaks: 1 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 5, 'ARG:plan': 6, 'TYR:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' CL': 1, 'NMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.33, per 1000 atoms: 0.24 Number of scatterers: 5534 At special positions: 0 Unit cell: (76.112, 81.472, 110.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 38 16.00 O 967 8.00 N 870 7.00 C 3658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 344.5 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 60.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.816A pdb=" N THR H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.121A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.754A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.837A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.992A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 153 removed outlier: 3.649A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.933A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.064A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 244 through 267 removed outlier: 4.167A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.856A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 removed outlier: 3.546A pdb=" N GLU A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 302 removed outlier: 3.618A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.921A pdb=" N ASN A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.677A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.749A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.694A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 removed outlier: 3.940A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.823A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.567A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.909A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 571 through 581 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.546A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.761A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 6 removed outlier: 6.084A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N SER L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N SER L 68 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 12.035A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 12.066A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.179A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TRP L 36 " --> pdb=" O TRP L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.547A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 531 through 532 335 hydrogen bonds defined for protein. 930 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: 0.94 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 839 1.29 - 1.42: 1668 1.42 - 1.55: 3137 1.55 - 1.69: 1 1.69 - 1.82: 54 Bond restraints: 5699 Sorted by residual: bond pdb=" C GLU A 406 " pdb=" O GLU A 406 " ideal model delta sigma weight residual 1.236 1.160 0.076 1.29e-02 6.01e+03 3.48e+01 bond pdb=" CA GLU A 406 " pdb=" CB GLU A 406 " ideal model delta sigma weight residual 1.529 1.444 0.086 1.63e-02 3.76e+03 2.76e+01 bond pdb=" C HIS A 170 " pdb=" O HIS A 170 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.35e-02 5.49e+03 2.60e+01 bond pdb=" CZ NMG A 702 " pdb=" NH1 NMG A 702 " ideal model delta sigma weight residual 1.343 1.251 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" NE NMG A 702 " pdb=" CZ NMG A 702 " ideal model delta sigma weight residual 1.362 1.451 -0.089 2.00e-02 2.50e+03 1.99e+01 ... (remaining 5694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 7530 2.13 - 4.26: 250 4.26 - 6.40: 23 6.40 - 8.53: 2 8.53 - 10.66: 2 Bond angle restraints: 7807 Sorted by residual: angle pdb=" C HIS A 170 " pdb=" CA HIS A 170 " pdb=" CB HIS A 170 " ideal model delta sigma weight residual 110.11 99.46 10.65 1.90e+00 2.77e-01 3.14e+01 angle pdb=" CG1 VAL H 37 " pdb=" CB VAL H 37 " pdb=" CG2 VAL H 37 " ideal model delta sigma weight residual 110.80 121.46 -10.66 2.20e+00 2.07e-01 2.35e+01 angle pdb=" CA LEU A 396 " pdb=" C LEU A 396 " pdb=" N LEU A 397 " ideal model delta sigma weight residual 117.02 122.01 -4.99 1.17e+00 7.31e-01 1.82e+01 angle pdb=" N GLY A 76 " pdb=" CA GLY A 76 " pdb=" C GLY A 76 " ideal model delta sigma weight residual 111.67 115.57 -3.90 9.20e-01 1.18e+00 1.80e+01 angle pdb=" CA VAL H 37 " pdb=" CB VAL H 37 " pdb=" CG2 VAL H 37 " ideal model delta sigma weight residual 110.40 116.92 -6.52 1.70e+00 3.46e-01 1.47e+01 ... (remaining 7802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2917 17.44 - 34.88: 208 34.88 - 52.32: 57 52.32 - 69.75: 9 69.75 - 87.19: 5 Dihedral angle restraints: 3196 sinusoidal: 1063 harmonic: 2133 Sorted by residual: dihedral pdb=" CA PHE A 58 " pdb=" C PHE A 58 " pdb=" N VAL A 59 " pdb=" CA VAL A 59 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" C HIS A 170 " pdb=" N HIS A 170 " pdb=" CA HIS A 170 " pdb=" CB HIS A 170 " ideal model delta harmonic sigma weight residual -122.60 -111.79 -10.81 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" CA PRO A 280 " pdb=" C PRO A 280 " pdb=" N ASP A 281 " pdb=" CA ASP A 281 " ideal model delta harmonic sigma weight residual 180.00 158.92 21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 3193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 886 0.276 - 0.553: 2 0.553 - 0.829: 0 0.829 - 1.105: 0 1.105 - 1.382: 1 Chirality restraints: 889 Sorted by residual: chirality pdb=" CB VAL H 37 " pdb=" CA VAL H 37 " pdb=" CG1 VAL H 37 " pdb=" CG2 VAL H 37 " both_signs ideal model delta sigma weight residual False -2.63 -1.25 -1.38 2.00e-01 2.50e+01 4.77e+01 chirality pdb=" CA ARG A 66 " pdb=" N ARG A 66 " pdb=" C ARG A 66 " pdb=" CB ARG A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA PHE A 58 " pdb=" N PHE A 58 " pdb=" C PHE A 58 " pdb=" CB PHE A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 886 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 65 " 0.175 2.00e-02 2.50e+03 9.26e-02 2.14e+02 pdb=" CG TRP A 65 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP A 65 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP A 65 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP A 65 " -0.068 2.00e-02 2.50e+03 pdb=" CE2 TRP A 65 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 65 " -0.108 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 65 " 0.134 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 65 " -0.067 2.00e-02 2.50e+03 pdb=" CH2 TRP A 65 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 138 " 0.172 2.00e-02 2.50e+03 9.65e-02 1.86e+02 pdb=" CG TYR A 138 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 138 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 TYR A 138 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR A 138 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR A 138 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR A 138 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 138 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 291 " -0.061 2.00e-02 2.50e+03 3.37e-02 2.84e+01 pdb=" CG TRP A 291 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP A 291 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 291 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP A 291 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP A 291 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 291 " 0.058 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 291 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 291 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 291 " -0.047 2.00e-02 2.50e+03 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 45 2.61 - 3.18: 5036 3.18 - 3.76: 8776 3.76 - 4.33: 12459 4.33 - 4.90: 20930 Nonbonded interactions: 47246 Sorted by model distance: nonbonded pdb=" OG SER H 52 " pdb=" OE2 GLU A 490 " model vdw 2.040 3.040 nonbonded pdb=" NH2 ARG H 56 " pdb=" OD1 ASP A 491 " model vdw 2.101 3.120 nonbonded pdb=" N GLU A 114 " pdb=" OE1 GLU A 114 " model vdw 2.144 3.120 nonbonded pdb=" OG1 THR A 168 " pdb=" OE1 GLU A 197 " model vdw 2.222 3.040 nonbonded pdb=" O SER A 548 " pdb=" OG SER A 552 " model vdw 2.303 3.040 ... (remaining 47241 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.220 Find NCS groups from input model: 0.010 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.013 0.864 5703 Z= 1.189 Angle : 0.771 10.659 7813 Z= 0.487 Chirality : 0.067 1.382 889 Planarity : 0.007 0.097 970 Dihedral : 13.973 87.193 1835 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.93 % Allowed : 15.08 % Favored : 83.99 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.31), residues: 738 helix: 1.06 (0.27), residues: 369 sheet: 0.91 (0.55), residues: 99 loop : -0.66 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 104 TYR 0.172 0.004 TYR A 138 PHE 0.052 0.003 PHE A 79 TRP 0.175 0.005 TRP A 65 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 5699) covalent geometry : angle 0.77119 ( 7807) SS BOND : bond 0.00056 ( 3) SS BOND : angle 0.42105 ( 6) hydrogen bonds : bond 0.21847 ( 332) hydrogen bonds : angle 7.41984 ( 930) Misc. bond : bond 0.86408 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.187 Fit side-chains REVERT: H 59 TYR cc_start: 0.6981 (m-80) cc_final: 0.6690 (m-80) REVERT: A 69 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7913 (t80) REVERT: A 284 ARG cc_start: 0.8143 (tpp-160) cc_final: 0.7650 (tpt90) REVERT: A 309 MET cc_start: 0.7340 (mmp) cc_final: 0.6855 (mmp) REVERT: A 459 ASP cc_start: 0.8409 (t0) cc_final: 0.8152 (t0) REVERT: A 494 ASP cc_start: 0.8545 (t0) cc_final: 0.8174 (t70) outliers start: 5 outliers final: 2 residues processed: 113 average time/residue: 0.3729 time to fit residues: 44.8599 Evaluate side-chains 97 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 353 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 164 HIS ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.134756 restraints weight = 6666.711| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.78 r_work: 0.3509 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5703 Z= 0.146 Angle : 0.584 10.402 7813 Z= 0.305 Chirality : 0.042 0.219 889 Planarity : 0.005 0.041 970 Dihedral : 5.898 59.592 809 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.47 % Allowed : 13.41 % Favored : 82.12 % 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: 1.19 (0.32), residues: 738 helix: 1.80 (0.27), residues: 369 sheet: 0.83 (0.57), residues: 87 loop : -0.56 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 104 TYR 0.018 0.002 TYR A 69 PHE 0.013 0.002 PHE A 276 TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5699) covalent geometry : angle 0.58382 ( 7807) SS BOND : bond 0.00331 ( 3) SS BOND : angle 1.14125 ( 6) hydrogen bonds : bond 0.04445 ( 332) hydrogen bonds : angle 5.05363 ( 930) Misc. bond : bond 0.00236 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.210 Fit side-chains REVERT: H 59 TYR cc_start: 0.7717 (m-80) cc_final: 0.7431 (m-80) REVERT: L 95 TYR cc_start: 0.5369 (OUTLIER) cc_final: 0.4992 (t80) REVERT: A 69 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.7759 (t80) REVERT: A 267 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6535 (mm) REVERT: A 284 ARG cc_start: 0.8345 (tpp-160) cc_final: 0.7677 (tpt90) REVERT: A 309 MET cc_start: 0.7199 (mmp) cc_final: 0.6786 (mmp) REVERT: A 333 ASN cc_start: 0.7996 (t0) cc_final: 0.7706 (t0) REVERT: A 506 TYR cc_start: 0.8134 (m-80) cc_final: 0.7890 (m-80) outliers start: 24 outliers final: 8 residues processed: 114 average time/residue: 0.3805 time to fit residues: 46.3105 Evaluate side-chains 100 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 447 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.148393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127803 restraints weight = 6753.964| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.74 r_work: 0.3412 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5703 Z= 0.211 Angle : 0.631 9.020 7813 Z= 0.325 Chirality : 0.044 0.241 889 Planarity : 0.005 0.042 970 Dihedral : 6.165 58.716 806 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.84 % Allowed : 13.41 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.31), residues: 738 helix: 1.41 (0.27), residues: 371 sheet: 0.37 (0.56), residues: 88 loop : -0.64 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 98 TYR 0.023 0.002 TYR L 95 PHE 0.015 0.002 PHE A 276 TRP 0.014 0.002 TRP A 113 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 5699) covalent geometry : angle 0.62965 ( 7807) SS BOND : bond 0.00216 ( 3) SS BOND : angle 1.77098 ( 6) hydrogen bonds : bond 0.04607 ( 332) hydrogen bonds : angle 4.91474 ( 930) Misc. bond : bond 0.00105 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.203 Fit side-chains REVERT: H 59 TYR cc_start: 0.8692 (m-80) cc_final: 0.8344 (m-80) REVERT: H 108 TYR cc_start: 0.8974 (m-80) cc_final: 0.8771 (m-80) REVERT: L 95 TYR cc_start: 0.5843 (OUTLIER) cc_final: 0.5368 (t80) REVERT: A 66 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8873 (ttt-90) REVERT: A 114 GLU cc_start: 0.8022 (mp0) cc_final: 0.7720 (mp0) REVERT: A 284 ARG cc_start: 0.8387 (tpp-160) cc_final: 0.7743 (tpt90) REVERT: A 380 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8128 (mtp) REVERT: A 441 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8168 (mm) REVERT: A 506 TYR cc_start: 0.8324 (m-80) cc_final: 0.8096 (m-80) REVERT: A 521 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8266 (mm) outliers start: 26 outliers final: 14 residues processed: 113 average time/residue: 0.3646 time to fit residues: 44.1234 Evaluate side-chains 103 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 548 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 24 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.151438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130805 restraints weight = 6692.424| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.75 r_work: 0.3449 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5703 Z= 0.133 Angle : 0.540 7.120 7813 Z= 0.279 Chirality : 0.041 0.202 889 Planarity : 0.004 0.037 970 Dihedral : 5.641 59.448 806 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.28 % Allowed : 15.83 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.31), residues: 738 helix: 1.54 (0.27), residues: 372 sheet: 0.34 (0.56), residues: 88 loop : -0.61 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 104 TYR 0.018 0.001 TYR A 69 PHE 0.012 0.001 PHE A 276 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5699) covalent geometry : angle 0.53853 ( 7807) SS BOND : bond 0.00264 ( 3) SS BOND : angle 1.46124 ( 6) hydrogen bonds : bond 0.03789 ( 332) hydrogen bonds : angle 4.68855 ( 930) Misc. bond : bond 0.00102 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.185 Fit side-chains REVERT: H 59 TYR cc_start: 0.8704 (m-80) cc_final: 0.8224 (m-80) REVERT: H 108 TYR cc_start: 0.9039 (m-80) cc_final: 0.8802 (m-80) REVERT: A 69 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.7627 (t80) REVERT: A 114 GLU cc_start: 0.7902 (mp0) cc_final: 0.7691 (mp0) REVERT: A 267 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6761 (mm) REVERT: A 284 ARG cc_start: 0.8390 (tpp-160) cc_final: 0.7754 (tpt90) REVERT: A 441 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8197 (mm) REVERT: A 506 TYR cc_start: 0.8353 (m-80) cc_final: 0.8148 (m-80) outliers start: 23 outliers final: 9 residues processed: 106 average time/residue: 0.3575 time to fit residues: 40.6267 Evaluate side-chains 96 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.148341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127443 restraints weight = 6724.839| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.78 r_work: 0.3427 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5703 Z= 0.176 Angle : 0.573 7.914 7813 Z= 0.295 Chirality : 0.042 0.227 889 Planarity : 0.005 0.047 970 Dihedral : 5.834 59.266 806 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.03 % Allowed : 15.46 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.31), residues: 738 helix: 1.44 (0.27), residues: 372 sheet: 0.16 (0.56), residues: 88 loop : -0.71 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 66 TYR 0.027 0.002 TYR L 95 PHE 0.012 0.002 PHE A 276 TRP 0.015 0.001 TRP A 113 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 5699) covalent geometry : angle 0.57164 ( 7807) SS BOND : bond 0.00224 ( 3) SS BOND : angle 1.60506 ( 6) hydrogen bonds : bond 0.04091 ( 332) hydrogen bonds : angle 4.75127 ( 930) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.210 Fit side-chains REVERT: H 108 TYR cc_start: 0.9069 (m-80) cc_final: 0.8817 (m-80) REVERT: L 95 TYR cc_start: 0.5588 (OUTLIER) cc_final: 0.5086 (t80) REVERT: A 98 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8324 (mt-10) REVERT: A 114 GLU cc_start: 0.7858 (mp0) cc_final: 0.7572 (mp0) REVERT: A 284 ARG cc_start: 0.8388 (tpp-160) cc_final: 0.7747 (tpt90) REVERT: A 380 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8130 (mtp) REVERT: A 394 MET cc_start: 0.8381 (tmm) cc_final: 0.8154 (ttt) REVERT: A 441 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8170 (mm) REVERT: A 506 TYR cc_start: 0.8419 (m-80) cc_final: 0.8186 (m-80) outliers start: 27 outliers final: 17 residues processed: 110 average time/residue: 0.3573 time to fit residues: 42.1185 Evaluate side-chains 106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.149460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.128884 restraints weight = 6765.907| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.75 r_work: 0.3431 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5703 Z= 0.155 Angle : 0.555 7.646 7813 Z= 0.285 Chirality : 0.041 0.216 889 Planarity : 0.004 0.045 970 Dihedral : 5.684 59.559 806 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.66 % Allowed : 16.76 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.31), residues: 738 helix: 1.53 (0.27), residues: 372 sheet: 0.05 (0.56), residues: 88 loop : -0.73 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 66 TYR 0.022 0.002 TYR L 95 PHE 0.012 0.002 PHE A 276 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 5699) covalent geometry : angle 0.55330 ( 7807) SS BOND : bond 0.00246 ( 3) SS BOND : angle 1.46621 ( 6) hydrogen bonds : bond 0.03828 ( 332) hydrogen bonds : angle 4.68489 ( 930) Misc. bond : bond 0.00114 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.237 Fit side-chains REVERT: H 108 TYR cc_start: 0.9137 (m-80) cc_final: 0.8879 (m-80) REVERT: A 114 GLU cc_start: 0.7862 (mp0) cc_final: 0.7559 (mp0) REVERT: A 207 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8312 (m) REVERT: A 284 ARG cc_start: 0.8380 (tpp-160) cc_final: 0.7747 (tpt90) REVERT: A 394 MET cc_start: 0.8402 (tmm) cc_final: 0.8197 (ttt) REVERT: A 441 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8079 (mm) REVERT: A 506 TYR cc_start: 0.8439 (m-80) cc_final: 0.8200 (m-80) outliers start: 25 outliers final: 16 residues processed: 105 average time/residue: 0.3720 time to fit residues: 41.8086 Evaluate side-chains 100 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.148183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127674 restraints weight = 6810.330| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.75 r_work: 0.3410 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5703 Z= 0.187 Angle : 0.599 8.759 7813 Z= 0.305 Chirality : 0.043 0.235 889 Planarity : 0.005 0.053 970 Dihedral : 5.507 58.739 804 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.66 % Allowed : 17.32 % Favored : 78.03 % 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: 0.63 (0.31), residues: 738 helix: 1.46 (0.26), residues: 370 sheet: -0.05 (0.56), residues: 88 loop : -0.79 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 66 TYR 0.028 0.002 TYR L 95 PHE 0.014 0.002 PHE A 392 TRP 0.013 0.001 TRP A 470 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 5699) covalent geometry : angle 0.59787 ( 7807) SS BOND : bond 0.00219 ( 3) SS BOND : angle 1.54980 ( 6) hydrogen bonds : bond 0.04087 ( 332) hydrogen bonds : angle 4.77417 ( 930) Misc. bond : bond 0.00126 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.209 Fit side-chains REVERT: H 108 TYR cc_start: 0.9142 (m-80) cc_final: 0.8869 (m-80) REVERT: A 114 GLU cc_start: 0.7836 (mp0) cc_final: 0.7509 (mp0) REVERT: A 284 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.7739 (tpt90) REVERT: A 380 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8116 (mtp) REVERT: A 441 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8075 (mm) REVERT: A 506 TYR cc_start: 0.8466 (m-80) cc_final: 0.8206 (m-80) outliers start: 25 outliers final: 18 residues processed: 102 average time/residue: 0.3451 time to fit residues: 37.8762 Evaluate side-chains 107 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.148504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127889 restraints weight = 6748.475| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.76 r_work: 0.3420 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5703 Z= 0.172 Angle : 0.606 11.126 7813 Z= 0.303 Chirality : 0.043 0.231 889 Planarity : 0.004 0.046 970 Dihedral : 5.469 58.996 804 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.47 % Allowed : 17.69 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.31), residues: 738 helix: 1.49 (0.27), residues: 370 sheet: -0.06 (0.56), residues: 88 loop : -0.83 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 66 TYR 0.026 0.002 TYR L 95 PHE 0.012 0.002 PHE A 276 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 5699) covalent geometry : angle 0.60536 ( 7807) SS BOND : bond 0.00236 ( 3) SS BOND : angle 1.45544 ( 6) hydrogen bonds : bond 0.03954 ( 332) hydrogen bonds : angle 4.75759 ( 930) Misc. bond : bond 0.00130 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.220 Fit side-chains REVERT: H 108 TYR cc_start: 0.9161 (m-80) cc_final: 0.8886 (m-80) REVERT: A 114 GLU cc_start: 0.7851 (mp0) cc_final: 0.7518 (mp0) REVERT: A 284 ARG cc_start: 0.8377 (tpp-160) cc_final: 0.7743 (tpt90) REVERT: A 441 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8127 (mm) REVERT: A 506 TYR cc_start: 0.8480 (m-80) cc_final: 0.8264 (m-80) outliers start: 24 outliers final: 18 residues processed: 98 average time/residue: 0.3098 time to fit residues: 32.7966 Evaluate side-chains 98 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 0.0670 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.0370 chunk 61 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.152282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132024 restraints weight = 6757.138| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.76 r_work: 0.3468 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5703 Z= 0.115 Angle : 0.558 10.464 7813 Z= 0.277 Chirality : 0.040 0.184 889 Planarity : 0.004 0.051 970 Dihedral : 5.038 59.017 804 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.98 % Allowed : 19.37 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.31), residues: 738 helix: 1.71 (0.27), residues: 370 sheet: -0.04 (0.56), residues: 88 loop : -0.80 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.021 0.001 TYR L 95 PHE 0.015 0.001 PHE A 150 TRP 0.019 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5699) covalent geometry : angle 0.55766 ( 7807) SS BOND : bond 0.00266 ( 3) SS BOND : angle 1.12281 ( 6) hydrogen bonds : bond 0.03413 ( 332) hydrogen bonds : angle 4.55376 ( 930) Misc. bond : bond 0.00111 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.214 Fit side-chains REVERT: H 108 TYR cc_start: 0.9117 (m-80) cc_final: 0.8844 (m-80) REVERT: A 69 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.7740 (t80) REVERT: A 114 GLU cc_start: 0.7834 (mp0) cc_final: 0.7475 (mp0) REVERT: A 207 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8319 (m) REVERT: A 267 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6937 (mm) REVERT: A 284 ARG cc_start: 0.8349 (tpp-160) cc_final: 0.7724 (tpt90) REVERT: A 441 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8123 (mm) outliers start: 16 outliers final: 10 residues processed: 99 average time/residue: 0.3459 time to fit residues: 36.8869 Evaluate side-chains 96 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 64 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** 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 = 0.3835 r_free = 0.3835 target = 0.151050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130624 restraints weight = 6748.287| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.76 r_work: 0.3455 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5703 Z= 0.133 Angle : 0.579 10.333 7813 Z= 0.287 Chirality : 0.042 0.208 889 Planarity : 0.004 0.051 970 Dihedral : 5.123 58.718 804 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.79 % Allowed : 21.04 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.31), residues: 738 helix: 1.69 (0.27), residues: 370 sheet: -0.11 (0.56), residues: 88 loop : -0.83 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.018 0.001 TYR L 95 PHE 0.012 0.001 PHE A 338 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5699) covalent geometry : angle 0.57807 ( 7807) SS BOND : bond 0.00240 ( 3) SS BOND : angle 1.16643 ( 6) hydrogen bonds : bond 0.03589 ( 332) hydrogen bonds : angle 4.59038 ( 930) Misc. bond : bond 0.00114 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.223 Fit side-chains REVERT: H 108 TYR cc_start: 0.9134 (m-80) cc_final: 0.8855 (m-80) REVERT: A 114 GLU cc_start: 0.7860 (mp0) cc_final: 0.7521 (mp0) REVERT: A 207 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8335 (m) REVERT: A 284 ARG cc_start: 0.8379 (tpp-160) cc_final: 0.7760 (tpt90) REVERT: A 327 MET cc_start: 0.7740 (mmp) cc_final: 0.7489 (mmp) REVERT: A 441 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8128 (mm) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.3498 time to fit residues: 35.4348 Evaluate side-chains 95 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 51 optimal weight: 0.0170 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131677 restraints weight = 6744.632| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.74 r_work: 0.3465 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5703 Z= 0.124 Angle : 0.574 11.637 7813 Z= 0.283 Chirality : 0.041 0.221 889 Planarity : 0.004 0.052 970 Dihedral : 5.047 58.563 804 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.35 % Allowed : 20.86 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.31), residues: 738 helix: 1.72 (0.27), residues: 370 sheet: -0.13 (0.56), residues: 88 loop : -0.82 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.018 0.001 TYR L 95 PHE 0.016 0.001 PHE A 150 TRP 0.017 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5699) covalent geometry : angle 0.57308 ( 7807) SS BOND : bond 0.00238 ( 3) SS BOND : angle 1.10763 ( 6) hydrogen bonds : bond 0.03504 ( 332) hydrogen bonds : angle 4.55855 ( 930) Misc. bond : bond 0.00111 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.62 seconds wall clock time: 31 minutes 57.97 seconds (1917.97 seconds total)