Starting phenix.real_space_refine on Tue Feb 3 17:28:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k21_61987/02_2026/9k21_61987.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k21_61987/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9k21_61987/02_2026/9k21_61987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k21_61987/02_2026/9k21_61987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k21_61987/02_2026/9k21_61987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k21_61987/02_2026/9k21_61987.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 9 Unusual residues: {' CL': 1, 'A20': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.10, per 1000 atoms: 0.20 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: 0.54 Conformation dependent library (CDL) restraints added in 493.4 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: 0.14 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: 0.67 Time building geometry restraints manager: 0.68 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.490 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 covalent geometry : bond 0.00531 ( 5652) covalent geometry : angle 0.88586 ( 7757) SS BOND : bond 0.00261 ( 3) SS BOND : angle 1.74464 ( 6) hydrogen bonds : bond 0.14874 ( 346) hydrogen bonds : angle 6.38095 ( 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: 0.0572 time to fit residues: 8.4698 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 : 0.130 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3462 r_free = 0.3462 target = 0.128821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.109852 restraints weight = 8102.697| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.82 r_work: 0.3088 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1623 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= 0.144 Angle : 0.592 7.566 7763 Z= 0.310 Chirality : 0.042 0.161 890 Planarity : 0.005 0.063 965 Dihedral : 6.917 126.635 806 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.33 % Allowed : 9.30 % 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: 0.75 (0.31), residues: 746 helix: 1.40 (0.27), residues: 365 sheet: -0.10 (0.53), residues: 88 loop : -0.38 (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 0.014 0.001 PHE A 345 TRP 0.021 0.001 TRP A 470 HIS 0.002 0.000 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5652) covalent geometry : angle 0.59129 ( 7757) SS BOND : bond 0.00623 ( 3) SS BOND : angle 1.39511 ( 6) hydrogen bonds : bond 0.04124 ( 346) hydrogen bonds : angle 4.77602 ( 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: 12 poor density : 97 time to evaluate : 0.121 Fit side-chains REVERT: H 65 THR cc_start: 0.8153 (t) cc_final: 0.7647 (m) REVERT: A 115 LYS cc_start: 0.8550 (mttp) cc_final: 0.8284 (mtmt) REVERT: A 151 GLN cc_start: 0.8321 (mm110) cc_final: 0.7975 (mm-40) REVERT: A 578 TYR cc_start: 0.8486 (t80) cc_final: 0.8181 (t80) outliers start: 12 outliers final: 9 residues processed: 104 average time/residue: 0.0530 time to fit residues: 7.5378 Evaluate side-chains 94 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 13 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 565 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 0.0570 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105993 restraints weight = 8150.969| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.14 r_work: 0.3088 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5655 Z= 0.154 Angle : 0.589 8.567 7763 Z= 0.300 Chirality : 0.041 0.153 890 Planarity : 0.005 0.055 965 Dihedral : 6.593 122.670 806 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.29 % Allowed : 10.47 % Favored : 86.24 % 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: 0.86 (0.31), residues: 746 helix: 1.57 (0.28), residues: 367 sheet: 0.03 (0.54), residues: 88 loop : -0.49 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 98 TYR 0.016 0.001 TYR A 69 PHE 0.022 0.002 PHE A 232 TRP 0.018 0.001 TRP A 470 HIS 0.008 0.002 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5652) covalent geometry : angle 0.58821 ( 7757) SS BOND : bond 0.00532 ( 3) SS BOND : angle 1.41783 ( 6) hydrogen bonds : bond 0.03985 ( 346) hydrogen bonds : angle 4.59782 ( 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 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.130 Fit side-chains REVERT: H 57 TYR cc_start: 0.8676 (m-10) cc_final: 0.8436 (m-10) REVERT: H 65 THR cc_start: 0.7849 (t) cc_final: 0.7283 (m) REVERT: L 21 MET cc_start: 0.8467 (mtm) cc_final: 0.8067 (mtp) REVERT: A 115 LYS cc_start: 0.8366 (mttp) cc_final: 0.8018 (mtmt) REVERT: A 151 GLN cc_start: 0.8321 (mm110) cc_final: 0.8059 (mm-40) REVERT: A 309 MET cc_start: 0.4889 (mmp) cc_final: 0.4324 (mmp) REVERT: A 578 TYR cc_start: 0.8656 (t80) cc_final: 0.8292 (t80) outliers start: 17 outliers final: 14 residues processed: 105 average time/residue: 0.0526 time to fit residues: 7.6445 Evaluate side-chains 99 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 211 ASP Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 390 LEU 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: 0.2980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.0170 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 63 optimal weight: 0.7980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111950 restraints weight = 7977.407| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.07 r_work: 0.3157 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5655 Z= 0.104 Angle : 0.526 6.523 7763 Z= 0.269 Chirality : 0.039 0.152 890 Planarity : 0.004 0.047 965 Dihedral : 6.058 112.579 806 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.71 % Allowed : 13.18 % Favored : 84.11 % 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: 1.04 (0.32), residues: 746 helix: 1.71 (0.27), residues: 374 sheet: 0.27 (0.55), residues: 93 loop : -0.51 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.013 0.001 TYR A 83 PHE 0.015 0.001 PHE H 29 TRP 0.017 0.001 TRP A 470 HIS 0.009 0.002 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 5652) covalent geometry : angle 0.52496 ( 7757) SS BOND : bond 0.00366 ( 3) SS BOND : angle 1.11104 ( 6) hydrogen bonds : bond 0.03415 ( 346) hydrogen bonds : angle 4.37215 ( 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: 14 poor density : 98 time to evaluate : 0.202 Fit side-chains REVERT: H 65 THR cc_start: 0.7737 (t) cc_final: 0.7179 (m) REVERT: A 74 ASN cc_start: 0.8507 (m-40) cc_final: 0.8232 (m110) REVERT: A 115 LYS cc_start: 0.8317 (mttp) cc_final: 0.8010 (mtmt) REVERT: A 151 GLN cc_start: 0.8273 (mm110) cc_final: 0.7989 (mm-40) REVERT: A 167 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8302 (t0) REVERT: A 256 MET cc_start: 0.8111 (tpp) cc_final: 0.7872 (tpp) REVERT: A 277 TYR cc_start: 0.8962 (t80) cc_final: 0.8663 (t80) REVERT: A 452 MET cc_start: 0.8453 (tpp) cc_final: 0.8247 (tpp) REVERT: A 487 ARG cc_start: 0.7216 (ttm-80) cc_final: 0.5281 (tpt170) REVERT: A 578 TYR cc_start: 0.8716 (t80) cc_final: 0.8399 (t80) outliers start: 14 outliers final: 10 residues processed: 109 average time/residue: 0.0572 time to fit residues: 8.7337 Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 167 ASN Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 390 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: 1.9990 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105216 restraints weight = 8378.171| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.18 r_work: 0.3067 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5655 Z= 0.195 Angle : 0.595 6.822 7763 Z= 0.303 Chirality : 0.042 0.142 890 Planarity : 0.004 0.048 965 Dihedral : 5.817 94.029 806 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.68 % Allowed : 13.76 % Favored : 82.56 % 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: 0.89 (0.32), residues: 746 helix: 1.57 (0.28), residues: 374 sheet: 0.14 (0.56), residues: 94 loop : -0.53 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 98 TYR 0.017 0.002 TYR A 69 PHE 0.026 0.002 PHE A 232 TRP 0.014 0.001 TRP A 470 HIS 0.006 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 5652) covalent geometry : angle 0.59399 ( 7757) SS BOND : bond 0.00548 ( 3) SS BOND : angle 1.36853 ( 6) hydrogen bonds : bond 0.03943 ( 346) hydrogen bonds : angle 4.53746 ( 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 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.131 Fit side-chains REVERT: H 65 THR cc_start: 0.7893 (t) cc_final: 0.7325 (m) REVERT: A 115 LYS cc_start: 0.8484 (mttp) cc_final: 0.8137 (mtmt) REVERT: A 151 GLN cc_start: 0.8436 (mm110) cc_final: 0.8104 (mm-40) REVERT: A 309 MET cc_start: 0.4788 (mmp) cc_final: 0.4258 (mmp) REVERT: A 487 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.5547 (tpt170) REVERT: A 495 MET cc_start: 0.8965 (mtm) cc_final: 0.8556 (mtm) REVERT: A 578 TYR cc_start: 0.8770 (t80) cc_final: 0.8501 (t80) outliers start: 19 outliers final: 15 residues processed: 100 average time/residue: 0.0507 time to fit residues: 7.0422 Evaluate side-chains 97 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108752 restraints weight = 8076.370| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.12 r_work: 0.3109 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2665 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= 0.135 Angle : 0.547 6.068 7763 Z= 0.278 Chirality : 0.040 0.138 890 Planarity : 0.004 0.044 965 Dihedral : 5.513 88.295 806 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.29 % Allowed : 14.53 % Favored : 82.17 % 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: 1.61 (0.28), residues: 374 sheet: 0.15 (0.56), residues: 94 loop : -0.52 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.014 0.001 TYR A 69 PHE 0.017 0.001 PHE A 232 TRP 0.015 0.001 TRP A 470 HIS 0.005 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5652) covalent geometry : angle 0.54659 ( 7757) SS BOND : bond 0.00406 ( 3) SS BOND : angle 1.15024 ( 6) hydrogen bonds : bond 0.03571 ( 346) hydrogen bonds : angle 4.41816 ( 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 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.196 Fit side-chains REVERT: H 65 THR cc_start: 0.7871 (t) cc_final: 0.7300 (m) REVERT: A 74 ASN cc_start: 0.8462 (m-40) cc_final: 0.8224 (m110) REVERT: A 115 LYS cc_start: 0.8477 (mttp) cc_final: 0.8132 (mtmt) REVERT: A 151 GLN cc_start: 0.8443 (mm110) cc_final: 0.8095 (mm-40) REVERT: A 309 MET cc_start: 0.5006 (mmp) cc_final: 0.4431 (mmp) REVERT: A 487 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.5513 (tpt170) REVERT: A 578 TYR cc_start: 0.8773 (t80) cc_final: 0.8546 (t80) outliers start: 17 outliers final: 15 residues processed: 98 average time/residue: 0.0536 time to fit residues: 7.2711 Evaluate side-chains 100 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 101 VAL 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 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: 2.9990 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.127007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106024 restraints weight = 8206.678| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.15 r_work: 0.3098 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2758 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= 0.152 Angle : 0.561 8.746 7763 Z= 0.283 Chirality : 0.040 0.137 890 Planarity : 0.004 0.043 965 Dihedral : 5.359 78.734 806 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.10 % Allowed : 16.47 % 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: 0.95 (0.32), residues: 746 helix: 1.60 (0.28), residues: 375 sheet: 0.18 (0.56), residues: 94 loop : -0.50 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.016 0.001 TYR A 69 PHE 0.014 0.001 PHE A 232 TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5652) covalent geometry : angle 0.56066 ( 7757) SS BOND : bond 0.00447 ( 3) SS BOND : angle 1.19304 ( 6) hydrogen bonds : bond 0.03624 ( 346) hydrogen bonds : angle 4.42655 ( 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 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.199 Fit side-chains REVERT: H 65 THR cc_start: 0.7866 (t) cc_final: 0.7277 (m) REVERT: L 2 ASN cc_start: 0.7861 (t0) cc_final: 0.7638 (t0) REVERT: A 74 ASN cc_start: 0.8465 (m-40) cc_final: 0.8194 (m110) REVERT: A 115 LYS cc_start: 0.8505 (mttp) cc_final: 0.8167 (mtmt) REVERT: A 151 GLN cc_start: 0.8367 (mm110) cc_final: 0.7959 (mm-40) REVERT: A 309 MET cc_start: 0.4934 (mmp) cc_final: 0.4382 (mmp) REVERT: A 390 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8689 (mm) REVERT: A 487 ARG cc_start: 0.7559 (ttm-80) cc_final: 0.5482 (tpt170) REVERT: A 578 TYR cc_start: 0.8746 (t80) cc_final: 0.8530 (t80) outliers start: 16 outliers final: 14 residues processed: 100 average time/residue: 0.0553 time to fit residues: 7.7148 Evaluate side-chains 98 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 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: 0.0870 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109451 restraints weight = 8105.795| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.06 r_work: 0.3147 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5655 Z= 0.107 Angle : 0.530 9.639 7763 Z= 0.265 Chirality : 0.039 0.133 890 Planarity : 0.004 0.041 965 Dihedral : 5.022 62.463 806 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.91 % Allowed : 16.67 % 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: 1.10 (0.32), residues: 746 helix: 1.76 (0.28), residues: 376 sheet: 0.20 (0.56), residues: 94 loop : -0.47 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.014 0.001 TYR A 83 PHE 0.013 0.001 PHE A 232 TRP 0.013 0.001 TRP A 470 HIS 0.005 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5652) covalent geometry : angle 0.52968 ( 7757) SS BOND : bond 0.00351 ( 3) SS BOND : angle 0.90163 ( 6) hydrogen bonds : bond 0.03266 ( 346) hydrogen bonds : angle 4.28323 ( 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 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.126 Fit side-chains REVERT: H 65 THR cc_start: 0.7840 (t) cc_final: 0.7263 (m) REVERT: A 115 LYS cc_start: 0.8421 (mttp) cc_final: 0.8088 (mtpp) REVERT: A 151 GLN cc_start: 0.8287 (mm110) cc_final: 0.7900 (mm-40) REVERT: A 277 TYR cc_start: 0.8990 (t80) cc_final: 0.8707 (t80) REVERT: A 309 MET cc_start: 0.4927 (mmp) cc_final: 0.4390 (mmp) REVERT: A 487 ARG cc_start: 0.7518 (ttm-80) cc_final: 0.5548 (tpt90) outliers start: 15 outliers final: 13 residues processed: 98 average time/residue: 0.0454 time to fit residues: 6.2326 Evaluate side-chains 100 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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 19 VAL Chi-restraints excluded: chain L residue 29 VAL 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 437 SER Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 13 optimal weight: 0.0870 chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3520 r_free = 0.3520 target = 0.130690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110063 restraints weight = 8105.226| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.08 r_work: 0.3154 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5655 Z= 0.109 Angle : 0.542 10.368 7763 Z= 0.270 Chirality : 0.039 0.130 890 Planarity : 0.004 0.040 965 Dihedral : 4.505 44.637 806 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.49 % Allowed : 17.05 % Favored : 79.46 % 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: 1.18 (0.32), residues: 746 helix: 1.86 (0.27), residues: 377 sheet: 0.23 (0.56), residues: 94 loop : -0.50 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.014 0.001 TYR A 83 PHE 0.012 0.001 PHE A 232 TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5652) covalent geometry : angle 0.54205 ( 7757) SS BOND : bond 0.00359 ( 3) SS BOND : angle 0.88129 ( 6) hydrogen bonds : bond 0.03253 ( 346) hydrogen bonds : angle 4.26364 ( 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 108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.140 Fit side-chains REVERT: H 3 GLN cc_start: 0.8265 (tt0) cc_final: 0.7809 (mm-40) REVERT: H 65 THR cc_start: 0.7850 (t) cc_final: 0.7281 (m) REVERT: A 115 LYS cc_start: 0.8405 (mttp) cc_final: 0.8080 (mtpp) REVERT: A 151 GLN cc_start: 0.8271 (mm110) cc_final: 0.7909 (mm-40) REVERT: A 277 TYR cc_start: 0.8970 (t80) cc_final: 0.8687 (t80) REVERT: A 309 MET cc_start: 0.4905 (mmp) cc_final: 0.4371 (mmp) REVERT: A 321 ASN cc_start: 0.6889 (t0) cc_final: 0.6685 (t0) REVERT: A 487 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.5526 (tpt90) outliers start: 18 outliers final: 15 residues processed: 100 average time/residue: 0.0596 time to fit residues: 8.2813 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL 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 437 SER Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.0270 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110558 restraints weight = 8123.823| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.14 r_work: 0.3143 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5655 Z= 0.114 Angle : 0.544 10.608 7763 Z= 0.271 Chirality : 0.039 0.130 890 Planarity : 0.004 0.040 965 Dihedral : 4.096 20.020 806 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: 1.19 (0.32), residues: 746 helix: 1.89 (0.27), residues: 377 sheet: 0.21 (0.56), residues: 94 loop : -0.52 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.014 0.001 TYR A 83 PHE 0.011 0.001 PHE A 232 TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5652) covalent geometry : angle 0.54360 ( 7757) SS BOND : bond 0.00383 ( 3) SS BOND : angle 0.89963 ( 6) hydrogen bonds : bond 0.03233 ( 346) hydrogen bonds : angle 4.27432 ( 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 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.204 Fit side-chains REVERT: H 3 GLN cc_start: 0.8191 (tt0) cc_final: 0.7720 (mm-40) REVERT: H 65 THR cc_start: 0.7818 (t) cc_final: 0.7249 (m) REVERT: L 19 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.8050 (m) REVERT: A 115 LYS cc_start: 0.8401 (mttp) cc_final: 0.8076 (mtpp) REVERT: A 151 GLN cc_start: 0.8248 (mm110) cc_final: 0.7906 (mm-40) REVERT: A 277 TYR cc_start: 0.8977 (t80) cc_final: 0.8696 (t80) REVERT: A 309 MET cc_start: 0.4869 (mmp) cc_final: 0.4347 (mmp) REVERT: A 321 ASN cc_start: 0.6961 (t0) cc_final: 0.6431 (t0) REVERT: A 487 ARG cc_start: 0.7513 (ttm-80) cc_final: 0.5506 (tpt90) outliers start: 16 outliers final: 15 residues processed: 97 average time/residue: 0.0654 time to fit residues: 8.7356 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 : 0.195 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL 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 381 MET Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 66 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109495 restraints weight = 8115.891| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.36 r_work: 0.3133 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5655 Z= 0.107 Angle : 0.537 10.623 7763 Z= 0.268 Chirality : 0.039 0.130 890 Planarity : 0.004 0.039 965 Dihedral : 3.958 19.680 806 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.29 % Allowed : 17.44 % 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: 1.22 (0.32), residues: 746 helix: 1.89 (0.27), residues: 379 sheet: 0.24 (0.56), residues: 94 loop : -0.50 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.014 0.001 TYR A 83 PHE 0.012 0.001 PHE A 338 TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 5652) covalent geometry : angle 0.53681 ( 7757) SS BOND : bond 0.00350 ( 3) SS BOND : angle 0.85032 ( 6) hydrogen bonds : bond 0.03155 ( 346) hydrogen bonds : angle 4.29035 ( 987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1184.80 seconds wall clock time: 21 minutes 1.26 seconds (1261.26 seconds total)