Starting phenix.real_space_refine on Thu Jul 2 02:03:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k21_61987/07_2026/9k21_61987.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k21_61987/07_2026/9k21_61987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k21_61987/07_2026/9k21_61987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k21_61987/07_2026/9k21_61987.map" model { file = "/net/cci-nas-00/data/ceres_data/9k21_61987/07_2026/9k21_61987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k21_61987/07_2026/9k21_61987.cif" } resolution = 3.45 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= 0.065 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 37 5.16 5 Cl 1 4.86 5 C 3625 2.51 5 N 860 2.21 5 O 966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5489 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 825 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 6, 'ASP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "L" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 723 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 5 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: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3932 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 27, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 9, 'ASN:plan1': 5, 'HIS:plan': 2, 'ARG:plan': 7, 'TYR:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 172 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'A20': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 1.16, per 1000 atoms: 0.21 Number of scatterers: 5489 At special positions: 0 Unit cell: (80.4, 80.4, 107.2, 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 37 16.00 O 966 8.00 N 860 7.00 C 3625 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=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 215.2 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 60.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.718A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.893A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 105 removed outlier: 3.807A pdb=" N GLY H 105 " --> pdb=" O ARG H 102 " (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 Processing helix chain 'A' and resid 48 through 59 removed outlier: 4.223A pdb=" N PHE A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.855A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 78 removed outlier: 4.095A pdb=" N ALA A 78 " --> pdb=" O GLY A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 78' Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.568A pdb=" N PHE A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 106 Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.263A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.150A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 266 Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.647A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 303 removed outlier: 4.360A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.796A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 354 removed outlier: 3.791A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.506A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.600A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 425 through 444 removed outlier: 4.285A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 448 Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.747A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.704A 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 removed outlier: 3.811A pdb=" N PHE A 520 " --> pdb=" O CYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 581 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.209A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.209A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.188A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP L 36 " --> pdb=" O TRP L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 11 removed outlier: 4.191A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 987 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: 0.66 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1429 1.33 - 1.46: 1271 1.46 - 1.58: 2901 1.58 - 1.70: 0 1.70 - 1.82: 51 Bond restraints: 5652 Sorted by residual: bond pdb=" N GLY A 89 " pdb=" CA GLY A 89 " ideal model delta sigma weight residual 1.446 1.481 -0.035 1.53e-02 4.27e+03 5.31e+00 bond pdb=" N PRO A 82 " pdb=" CD PRO A 82 " ideal model delta sigma weight residual 1.473 1.443 0.030 1.40e-02 5.10e+03 4.66e+00 bond pdb=" CAG A20 A 702 " pdb=" SAH A20 A 702 " ideal model delta sigma weight residual 1.800 1.758 0.042 2.00e-02 2.50e+03 4.36e+00 bond pdb=" N PRO A 93 " pdb=" CD PRO A 93 " ideal model delta sigma weight residual 1.473 1.444 0.029 1.40e-02 5.10e+03 4.15e+00 bond pdb=" N PRO A 367 " pdb=" CD PRO A 367 " ideal model delta sigma weight residual 1.473 1.444 0.029 1.40e-02 5.10e+03 4.15e+00 ... (remaining 5647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 7700 3.61 - 7.22: 52 7.22 - 10.82: 3 10.82 - 14.43: 1 14.43 - 18.04: 1 Bond angle restraints: 7757 Sorted by residual: angle pdb=" OAB A20 A 702 " pdb=" SAH A20 A 702 " pdb=" OAD A20 A 702 " ideal model delta sigma weight residual 112.91 94.87 18.04 3.00e+00 1.11e-01 3.62e+01 angle pdb=" CA PHE A 299 " pdb=" CB PHE A 299 " pdb=" CG PHE A 299 " ideal model delta sigma weight residual 113.80 118.61 -4.81 1.00e+00 1.00e+00 2.31e+01 angle pdb=" N LYS A 534 " pdb=" CA LYS A 534 " pdb=" C LYS A 534 " ideal model delta sigma weight residual 112.87 118.41 -5.54 1.20e+00 6.94e-01 2.13e+01 angle pdb=" C GLY A 366 " pdb=" N PRO A 367 " pdb=" CA PRO A 367 " ideal model delta sigma weight residual 119.84 125.42 -5.58 1.25e+00 6.40e-01 1.99e+01 angle pdb=" CAF A20 A 702 " pdb=" CAG A20 A 702 " pdb=" SAH A20 A 702 " ideal model delta sigma weight residual 113.22 99.85 13.37 3.00e+00 1.11e-01 1.99e+01 ... (remaining 7752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.30: 3030 25.30 - 50.60: 112 50.60 - 75.90: 11 75.90 - 101.20: 4 101.20 - 126.50: 1 Dihedral angle restraints: 3158 sinusoidal: 1001 harmonic: 2157 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 42.42 50.58 1 1.00e+01 1.00e-02 3.50e+01 dihedral pdb=" CA GLY A 89 " pdb=" C GLY A 89 " pdb=" N SER A 90 " pdb=" CA SER A 90 " ideal model delta harmonic sigma weight residual 180.00 150.88 29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ASN A 533 " pdb=" C ASN A 533 " pdb=" N LYS A 534 " pdb=" CA LYS A 534 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 3155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 729 0.056 - 0.112: 130 0.112 - 0.168: 24 0.168 - 0.225: 4 0.225 - 0.281: 3 Chirality restraints: 890 Sorted by residual: chirality pdb=" CA THR A 512 " pdb=" N THR A 512 " pdb=" C THR A 512 " pdb=" CB THR A 512 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA PRO A 513 " pdb=" N PRO A 513 " pdb=" C PRO A 513 " pdb=" CB PRO A 513 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA TYR A 532 " pdb=" N TYR A 532 " pdb=" C TYR A 532 " pdb=" CB TYR A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 887 not shown) Planarity restraints: 965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 532 " 0.171 2.00e-02 2.50e+03 9.50e-02 1.80e+02 pdb=" CG TYR A 532 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 532 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR A 532 " -0.080 2.00e-02 2.50e+03 pdb=" CE1 TYR A 532 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR A 532 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR A 532 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 532 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 302 " -0.142 2.00e-02 2.50e+03 8.24e-02 1.36e+02 pdb=" CG TYR A 302 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 302 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR A 302 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR A 302 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR A 302 " 0.052 2.00e-02 2.50e+03 pdb=" CZ TYR A 302 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 302 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 460 " -0.052 2.00e-02 2.50e+03 3.09e-02 1.91e+01 pdb=" CG TYR A 460 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 460 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 460 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 460 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 460 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 460 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 460 " -0.051 2.00e-02 2.50e+03 ... (remaining 962 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 69 2.69 - 3.24: 5700 3.24 - 3.79: 8516 3.79 - 4.35: 11451 4.35 - 4.90: 19419 Nonbonded interactions: 45155 Sorted by model distance: nonbonded pdb=" OG SER A 132 " pdb=" OE1 GLN A 410 " model vdw 2.134 3.040 nonbonded pdb=" O SER L 31 " pdb=" OG1 THR L 52 " model vdw 2.135 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OD1 ASN A 333 " model vdw 2.178 3.120 nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.240 3.040 nonbonded pdb=" OE2 GLU H 50 " pdb=" OH TYR L 95 " model vdw 2.314 3.040 ... (remaining 45150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.910 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5655 Z= 0.280 Angle : 0.887 18.039 7763 Z= 0.527 Chirality : 0.049 0.281 890 Planarity : 0.007 0.095 965 Dihedral : 13.150 126.505 1781 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.02 (0.30), residues: 746 helix: 0.53 (0.26), residues: 361 sheet: 0.20 (0.51), residues: 108 loop : -0.70 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 62 TYR 0.171 0.007 TYR A 532 PHE 0.042 0.003 PHE A 86 TRP 0.054 0.004 TRP A 291 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.28 ( 5652) covalent geometry : angle 0.88586 / 0.53 ( 7757) SS BOND : bond 0.00261 / 0.13 ( 3) SS BOND : angle 1.74464 / 0.93 ( 6) hydrogen bonds : bond 0.14874 / 9.61 ( 346) hydrogen bonds : angle 6.38095 / 4.51 ( 987) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.129 Fit side-chains REVERT: H 65 THR cc_start: 0.7980 (t) cc_final: 0.7440 (m) REVERT: A 151 GLN cc_start: 0.8027 (mm110) cc_final: 0.7673 (mm-40) REVERT: A 578 TYR cc_start: 0.8524 (t80) cc_final: 0.8149 (t80) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0587 time to fit residues: 8.8196 Evaluate side-chains 92 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 39 GLN A 63 ASN A 74 ASN A 212 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.109553 restraints weight = 8096.514| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.84 r_work: 0.3083 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5655 Z= 0.144 Angle : 0.596 7.703 7763 Z= 0.311 Chirality : 0.041 0.158 890 Planarity : 0.005 0.063 965 Dihedral : 6.914 125.097 806 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.52 % Allowed : 9.11 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 746 helix: 1.39 (0.27), residues: 365 sheet: -0.10 (0.54), residues: 88 loop : -0.39 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 62 TYR 0.017 0.001 TYR A 69 PHE 0.013 0.001 PHE A 345 TRP 0.021 0.002 TRP A 470 HIS 0.002 0.000 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 5652) covalent geometry : angle 0.59442 / 0.31 ( 7757) SS BOND : bond 0.00552 / 0.27 ( 3) SS BOND : angle 1.42229 / 0.79 ( 6) hydrogen bonds : bond 0.04209 / 2.73 ( 346) hydrogen bonds : angle 4.80431 / 3.39 ( 987) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.226 Fit side-chains REVERT: H 65 THR cc_start: 0.8163 (t) cc_final: 0.7657 (m) REVERT: A 115 LYS cc_start: 0.8616 (mttp) cc_final: 0.8319 (mtmt) REVERT: A 151 GLN cc_start: 0.8321 (mm110) cc_final: 0.7980 (mm-40) REVERT: A 578 TYR cc_start: 0.8480 (t80) cc_final: 0.8177 (t80) outliers start: 13 outliers final: 10 residues processed: 103 average time/residue: 0.0638 time to fit residues: 8.9899 Evaluate side-chains 94 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 6 GLN ** 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 = 0.3430 r_free = 0.3430 target = 0.123847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102984 restraints weight = 8205.135| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.17 r_work: 0.3031 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 5655 Z= 0.249 Angle : 0.671 8.533 7763 Z= 0.343 Chirality : 0.044 0.154 890 Planarity : 0.005 0.060 965 Dihedral : 6.663 114.706 806 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.49 % Allowed : 11.24 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.54 (0.31), residues: 746 helix: 1.36 (0.27), residues: 365 sheet: -0.20 (0.54), residues: 88 loop : -0.68 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 98 TYR 0.020 0.002 TYR A 69 PHE 0.022 0.002 PHE A 232 TRP 0.019 0.002 TRP A 470 HIS 0.010 0.002 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.25 ( 5652) covalent geometry : angle 0.66913 / 0.34 ( 7757) SS BOND : bond 0.00688 / 0.34 ( 3) SS BOND : angle 1.75125 / 1.01 ( 6) hydrogen bonds : bond 0.04555 / 2.96 ( 346) hydrogen bonds : angle 4.82299 / 3.39 ( 987) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.207 Fit side-chains REVERT: H 65 THR cc_start: 0.7959 (t) cc_final: 0.7352 (m) REVERT: A 115 LYS cc_start: 0.8527 (mttp) cc_final: 0.8157 (mtmt) REVERT: A 309 MET cc_start: 0.4765 (mmp) cc_final: 0.4287 (mmp) REVERT: A 578 TYR cc_start: 0.8740 (t80) cc_final: 0.8418 (t80) outliers start: 18 outliers final: 15 residues processed: 104 average time/residue: 0.0615 time to fit residues: 8.8066 Evaluate side-chains 96 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107069 restraints weight = 8055.546| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.10 r_work: 0.3110 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5655 Z= 0.129 Angle : 0.552 7.113 7763 Z= 0.283 Chirality : 0.040 0.150 890 Planarity : 0.004 0.051 965 Dihedral : 5.954 100.784 806 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.29 % Allowed : 12.79 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.85 (0.32), residues: 746 helix: 1.55 (0.28), residues: 373 sheet: 0.04 (0.55), residues: 93 loop : -0.53 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 62 TYR 0.020 0.001 TYR A 440 PHE 0.017 0.001 PHE H 29 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 5652) covalent geometry : angle 0.55141 / 0.28 ( 7757) SS BOND : bond 0.00421 / 0.21 ( 3) SS BOND : angle 1.27585 / 0.74 ( 6) hydrogen bonds : bond 0.03699 / 2.41 ( 346) hydrogen bonds : angle 4.49978 / 3.16 ( 987) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.205 Fit side-chains REVERT: H 32 TYR cc_start: 0.8733 (m-80) cc_final: 0.8408 (m-80) REVERT: H 65 THR cc_start: 0.7818 (t) cc_final: 0.7240 (m) REVERT: A 74 ASN cc_start: 0.8424 (m-40) cc_final: 0.8175 (m110) REVERT: A 115 LYS cc_start: 0.8439 (mttp) cc_final: 0.8095 (mtmt) REVERT: A 151 GLN cc_start: 0.8280 (mm110) cc_final: 0.8009 (mm-40) REVERT: A 487 ARG cc_start: 0.7363 (ttm-80) cc_final: 0.5346 (tpt170) REVERT: A 578 TYR cc_start: 0.8753 (t80) cc_final: 0.8530 (t80) outliers start: 17 outliers final: 14 residues processed: 107 average time/residue: 0.0558 time to fit residues: 8.3035 Evaluate side-chains 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.105319 restraints weight = 8383.151| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.16 r_work: 0.3097 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5655 Z= 0.139 Angle : 0.555 6.320 7763 Z= 0.282 Chirality : 0.040 0.142 890 Planarity : 0.004 0.047 965 Dihedral : 5.667 94.793 806 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.10 % Allowed : 13.95 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.94 (0.32), residues: 746 helix: 1.59 (0.28), residues: 374 sheet: 0.32 (0.56), residues: 96 loop : -0.56 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.031 0.001 TYR A 440 PHE 0.026 0.001 PHE A 232 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 5652) covalent geometry : angle 0.55378 / 0.28 ( 7757) SS BOND : bond 0.00475 / 0.24 ( 3) SS BOND : angle 1.18994 / 0.70 ( 6) hydrogen bonds : bond 0.03655 / 2.39 ( 346) hydrogen bonds : angle 4.43445 / 3.12 ( 987) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.209 Fit side-chains REVERT: H 32 TYR cc_start: 0.8776 (m-80) cc_final: 0.8460 (m-80) REVERT: H 65 THR cc_start: 0.7830 (t) cc_final: 0.7246 (m) REVERT: A 115 LYS cc_start: 0.8453 (mttp) cc_final: 0.8109 (mtmt) REVERT: A 151 GLN cc_start: 0.8385 (mm110) cc_final: 0.8088 (mm-40) REVERT: A 309 MET cc_start: 0.4963 (mmp) cc_final: 0.4392 (mmp) REVERT: A 487 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.5426 (tpt170) REVERT: A 578 TYR cc_start: 0.8743 (t80) cc_final: 0.8509 (t80) outliers start: 16 outliers final: 14 residues processed: 100 average time/residue: 0.0681 time to fit residues: 9.3915 Evaluate side-chains 98 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.0170 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110643 restraints weight = 8083.405| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.07 r_work: 0.3169 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5655 Z= 0.101 Angle : 0.525 8.186 7763 Z= 0.264 Chirality : 0.039 0.137 890 Planarity : 0.004 0.042 965 Dihedral : 5.290 86.864 806 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.91 % Allowed : 16.28 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.13 (0.32), residues: 746 helix: 1.75 (0.27), residues: 376 sheet: 0.39 (0.57), residues: 96 loop : -0.49 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.032 0.001 TYR A 440 PHE 0.019 0.001 PHE A 232 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 5652) covalent geometry : angle 0.52494 / 0.26 ( 7757) SS BOND : bond 0.00322 / 0.16 ( 3) SS BOND : angle 0.94688 / 0.55 ( 6) hydrogen bonds : bond 0.03235 / 2.11 ( 346) hydrogen bonds : angle 4.28075 / 3.01 ( 987) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: H 32 TYR cc_start: 0.8717 (m-80) cc_final: 0.8409 (m-80) REVERT: H 65 THR cc_start: 0.7811 (t) cc_final: 0.7249 (m) REVERT: H 102 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8325 (mtt-85) REVERT: A 74 ASN cc_start: 0.8426 (m-40) cc_final: 0.8197 (m110) REVERT: A 115 LYS cc_start: 0.8394 (mttp) cc_final: 0.8076 (mtpp) REVERT: A 277 TYR cc_start: 0.8981 (t80) cc_final: 0.8691 (t80) REVERT: A 309 MET cc_start: 0.4967 (mmp) cc_final: 0.4366 (mmp) REVERT: A 487 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.5520 (tpt90) outliers start: 15 outliers final: 13 residues processed: 107 average time/residue: 0.0655 time to fit residues: 9.6654 Evaluate side-chains 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 562 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106036 restraints weight = 8259.141| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.15 r_work: 0.3094 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5655 Z= 0.157 Angle : 0.565 8.738 7763 Z= 0.285 Chirality : 0.040 0.133 890 Planarity : 0.004 0.042 965 Dihedral : 5.236 73.158 806 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.88 % Allowed : 15.70 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.05 (0.32), residues: 746 helix: 1.72 (0.28), residues: 375 sheet: 0.36 (0.57), residues: 96 loop : -0.56 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 98 TYR 0.034 0.002 TYR A 440 PHE 0.014 0.001 PHE A 345 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 5652) covalent geometry : angle 0.56405 / 0.28 ( 7757) SS BOND : bond 0.00469 / 0.23 ( 3) SS BOND : angle 1.18460 / 0.69 ( 6) hydrogen bonds : bond 0.03591 / 2.35 ( 346) hydrogen bonds : angle 4.37788 / 3.08 ( 987) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.253 Fit side-chains REVERT: H 32 TYR cc_start: 0.8767 (m-80) cc_final: 0.8462 (m-80) REVERT: H 65 THR cc_start: 0.7867 (t) cc_final: 0.7274 (m) REVERT: A 58 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.6216 (t80) REVERT: A 74 ASN cc_start: 0.8469 (m-40) cc_final: 0.8191 (m110) REVERT: A 115 LYS cc_start: 0.8439 (mttp) cc_final: 0.8101 (mtmt) REVERT: A 161 HIS cc_start: 0.8384 (m-70) cc_final: 0.8142 (m-70) REVERT: A 277 TYR cc_start: 0.9018 (t80) cc_final: 0.8732 (t80) REVERT: A 309 MET cc_start: 0.4950 (mmp) cc_final: 0.4352 (mmp) REVERT: A 487 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.5531 (tpt170) REVERT: A 578 TYR cc_start: 0.8803 (t80) cc_final: 0.8593 (t80) outliers start: 20 outliers final: 15 residues processed: 103 average time/residue: 0.0668 time to fit residues: 9.4531 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 97 LEU 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 207 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 562 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109427 restraints weight = 8118.662| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.11 r_work: 0.3123 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5655 Z= 0.121 Angle : 0.551 9.446 7763 Z= 0.275 Chirality : 0.039 0.130 890 Planarity : 0.004 0.041 965 Dihedral : 5.082 58.102 806 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.68 % Allowed : 16.47 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.11 (0.32), residues: 746 helix: 1.78 (0.27), residues: 376 sheet: 0.39 (0.57), residues: 96 loop : -0.57 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.036 0.001 TYR A 440 PHE 0.013 0.001 PHE A 232 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 5652) covalent geometry : angle 0.55018 / 0.27 ( 7757) SS BOND : bond 0.00400 / 0.20 ( 3) SS BOND : angle 1.06661 / 0.63 ( 6) hydrogen bonds : bond 0.03383 / 2.22 ( 346) hydrogen bonds : angle 4.30911 / 3.03 ( 987) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.199 Fit side-chains REVERT: H 32 TYR cc_start: 0.8727 (m-80) cc_final: 0.8417 (m-80) REVERT: H 65 THR cc_start: 0.7817 (t) cc_final: 0.7241 (m) REVERT: L 19 VAL cc_start: 0.8448 (p) cc_final: 0.8239 (m) REVERT: A 58 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.6214 (t80) REVERT: A 115 LYS cc_start: 0.8420 (mttp) cc_final: 0.8081 (mtmt) REVERT: A 151 GLN cc_start: 0.8331 (mm110) cc_final: 0.7883 (mm-40) REVERT: A 161 HIS cc_start: 0.8417 (m-70) cc_final: 0.8145 (m-70) REVERT: A 277 TYR cc_start: 0.9010 (t80) cc_final: 0.8732 (t80) REVERT: A 309 MET cc_start: 0.4981 (mmp) cc_final: 0.4392 (mmp) REVERT: A 487 ARG cc_start: 0.7531 (ttm-80) cc_final: 0.5491 (tpt170) REVERT: A 578 TYR cc_start: 0.8814 (t80) cc_final: 0.8595 (t80) outliers start: 19 outliers final: 15 residues processed: 105 average time/residue: 0.0618 time to fit residues: 9.0996 Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 97 LEU 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 207 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 562 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN A 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106696 restraints weight = 8170.979| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.15 r_work: 0.3102 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5655 Z= 0.147 Angle : 0.568 10.045 7763 Z= 0.285 Chirality : 0.040 0.131 890 Planarity : 0.004 0.041 965 Dihedral : 4.580 37.712 806 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.29 % Allowed : 16.67 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.05 (0.32), residues: 746 helix: 1.75 (0.27), residues: 376 sheet: 0.35 (0.56), residues: 96 loop : -0.62 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.021 0.001 TYR A 578 PHE 0.012 0.001 PHE A 345 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 5652) covalent geometry : angle 0.56769 / 0.29 ( 7757) SS BOND : bond 0.00418 / 0.21 ( 3) SS BOND : angle 1.14812 / 0.67 ( 6) hydrogen bonds : bond 0.03564 / 2.34 ( 346) hydrogen bonds : angle 4.36245 / 3.07 ( 987) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.204 Fit side-chains REVERT: H 32 TYR cc_start: 0.8734 (m-80) cc_final: 0.8476 (m-80) REVERT: H 65 THR cc_start: 0.7857 (t) cc_final: 0.7277 (m) REVERT: L 19 VAL cc_start: 0.8498 (p) cc_final: 0.8286 (m) REVERT: L 21 MET cc_start: 0.8606 (mtm) cc_final: 0.8218 (mtp) REVERT: A 58 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.6249 (t80) REVERT: A 74 ASN cc_start: 0.8357 (m-40) cc_final: 0.8142 (m110) REVERT: A 115 LYS cc_start: 0.8445 (mttp) cc_final: 0.8096 (mtmt) REVERT: A 161 HIS cc_start: 0.8421 (m-70) cc_final: 0.8184 (m-70) REVERT: A 277 TYR cc_start: 0.9075 (t80) cc_final: 0.8805 (t80) REVERT: A 309 MET cc_start: 0.4925 (mmp) cc_final: 0.4362 (mmp) REVERT: A 487 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.5566 (tpt170) REVERT: A 495 MET cc_start: 0.8801 (mtm) cc_final: 0.8595 (mtm) outliers start: 17 outliers final: 16 residues processed: 97 average time/residue: 0.0657 time to fit residues: 8.8075 Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 97 LEU 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 207 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 562 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.0020 chunk 12 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN A 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.129668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108522 restraints weight = 8165.946| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.16 r_work: 0.3129 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5655 Z= 0.118 Angle : 0.551 10.577 7763 Z= 0.276 Chirality : 0.039 0.133 890 Planarity : 0.004 0.039 965 Dihedral : 4.162 21.486 806 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.10 % Allowed : 17.05 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.12 (0.32), residues: 746 helix: 1.80 (0.27), residues: 376 sheet: 0.37 (0.57), residues: 96 loop : -0.58 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.032 0.001 TYR A 578 PHE 0.012 0.001 PHE A 232 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 5652) covalent geometry : angle 0.55105 / 0.28 ( 7757) SS BOND : bond 0.00361 / 0.18 ( 3) SS BOND : angle 0.94333 / 0.56 ( 6) hydrogen bonds : bond 0.03377 / 2.20 ( 346) hydrogen bonds : angle 4.30176 / 3.04 ( 987) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.141 Fit side-chains REVERT: H 3 GLN cc_start: 0.8280 (tt0) cc_final: 0.7864 (mm-40) REVERT: H 32 TYR cc_start: 0.8715 (m-80) cc_final: 0.8431 (m-80) REVERT: H 65 THR cc_start: 0.7818 (t) cc_final: 0.7245 (m) REVERT: L 21 MET cc_start: 0.8568 (mtm) cc_final: 0.8138 (mtp) REVERT: A 58 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.6236 (t80) REVERT: A 74 ASN cc_start: 0.8375 (m-40) cc_final: 0.8117 (m110) REVERT: A 115 LYS cc_start: 0.8416 (mttp) cc_final: 0.8079 (mtmt) REVERT: A 151 GLN cc_start: 0.8293 (mm110) cc_final: 0.7852 (mm-40) REVERT: A 161 HIS cc_start: 0.8402 (m-70) cc_final: 0.8162 (m-70) REVERT: A 277 TYR cc_start: 0.9008 (t80) cc_final: 0.8738 (t80) REVERT: A 309 MET cc_start: 0.4902 (mmp) cc_final: 0.4332 (mmp) REVERT: A 440 TYR cc_start: 0.8395 (t80) cc_final: 0.8085 (t80) REVERT: A 487 ARG cc_start: 0.7518 (ttm-80) cc_final: 0.5479 (tpt170) outliers start: 16 outliers final: 14 residues processed: 98 average time/residue: 0.0609 time to fit residues: 8.1274 Evaluate side-chains 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 97 LEU 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 207 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 562 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107614 restraints weight = 8146.356| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.06 r_work: 0.3108 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5655 Z= 0.142 Angle : 0.568 10.750 7763 Z= 0.285 Chirality : 0.040 0.148 890 Planarity : 0.004 0.040 965 Dihedral : 4.242 21.742 806 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.10 % Allowed : 17.64 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.09 (0.32), residues: 746 helix: 1.79 (0.28), residues: 376 sheet: 0.32 (0.56), residues: 96 loop : -0.61 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 98 TYR 0.030 0.001 TYR A 578 PHE 0.012 0.001 PHE A 345 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 5652) covalent geometry : angle 0.56750 / 0.28 ( 7757) SS BOND : bond 0.00398 / 0.20 ( 3) SS BOND : angle 0.94388 / 0.56 ( 6) hydrogen bonds : bond 0.03505 / 2.30 ( 346) hydrogen bonds : angle 4.35630 / 3.07 ( 987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1380.18 seconds wall clock time: 24 minutes 25.59 seconds (1465.59 seconds total)