Starting phenix.real_space_refine on Tue Feb 3 16:52:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mte_48606/02_2026/9mte_48606.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mte_48606/02_2026/9mte_48606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mte_48606/02_2026/9mte_48606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mte_48606/02_2026/9mte_48606.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mte_48606/02_2026/9mte_48606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mte_48606/02_2026/9mte_48606.map" } resolution = 2.66 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= 0.001 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 3209 2.51 5 N 912 2.21 5 O 945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 5108 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3414 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 25, 'TRANS': 425} Chain breaks: 6 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 1.18, per 1000 atoms: 0.23 Number of scatterers: 5108 At special positions: 0 Unit cell: (83.52, 82.36, 100.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 945 8.00 N 912 7.00 C 3209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 53 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 195 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 199 " - pdb=" SG CYS C 212 " distance=2.02 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 227 " distance=2.03 Simple disulfide: pdb=" SG CYS C 224 " - pdb=" SG CYS C 235 " distance=2.03 Simple disulfide: pdb=" SG CYS C 236 " - pdb=" SG CYS C 244 " distance=2.03 Simple disulfide: pdb=" SG CYS C 240 " - pdb=" SG CYS C 252 " distance=2.03 Simple disulfide: pdb=" SG CYS C 255 " - pdb=" SG CYS C 264 " distance=2.03 Simple disulfide: pdb=" SG CYS C 268 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 299 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 342 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 504 " 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: 0.33 Conformation dependent library (CDL) restraints added in 333.9 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1234 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 14 sheets defined 14.0% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.572A pdb=" N ARG A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.959A pdb=" N THR A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.610A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.654A pdb=" N GLN C 75 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 Processing helix chain 'C' and resid 168 through 173 removed outlier: 3.864A pdb=" N ILE C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.880A pdb=" N CYS C 212 " --> pdb=" O SER C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.620A pdb=" N CYS C 235 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 365 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.601A pdb=" N ASP C 382 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.861A pdb=" N GLN C 398 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 399 " --> pdb=" O GLN C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 426 Processing helix chain 'C' and resid 436 through 439 Processing helix chain 'C' and resid 481 through 486 removed outlier: 3.513A pdb=" N LEU C 485 " --> pdb=" O PRO C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 528 removed outlier: 3.732A pdb=" N GLN C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 524 through 528' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.596A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.596A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.984A pdb=" N MET A 34 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 10 through 11 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 13 removed outlier: 7.009A pdb=" N MET B 35 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU B 51 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP B 37 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 13 Processing sheet with id=AA8, first strand: chain 'C' and resid 25 through 27 removed outlier: 6.862A pdb=" N CYS C 26 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 63 removed outlier: 6.425A pdb=" N LEU C 60 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ALA C 87 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU C 62 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLY C 152 " --> pdb=" O TYR C 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 258 through 260 Processing sheet with id=AB2, first strand: chain 'C' and resid 289 through 291 Processing sheet with id=AB3, first strand: chain 'C' and resid 311 through 312 removed outlier: 7.071A pdb=" N SER C 305 " --> pdb=" O CYS C 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 342 through 343 removed outlier: 7.316A pdb=" N CYS C 342 " --> pdb=" O PHE C 371 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 374 through 376 removed outlier: 6.125A pdb=" N LEU C 374 " --> pdb=" O TYR C 411 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU C 410 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLN C 446 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE C 412 " --> pdb=" O GLN C 446 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR C 441 " --> pdb=" O LEU C 465 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU C 467 " --> pdb=" O TYR C 441 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU C 443 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N HIS C 469 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU C 445 " --> pdb=" O HIS C 469 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA C 466 " --> pdb=" O LEU C 494 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR C 496 " --> pdb=" O ALA C 466 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 468 " --> pdb=" O THR C 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 156 hydrogen bonds defined for protein. 330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1711 1.35 - 1.46: 1203 1.46 - 1.58: 2252 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 5216 Sorted by residual: bond pdb=" C GLN B 45 " pdb=" N ARG B 46 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.46e-02 4.69e+03 6.48e+00 bond pdb=" CB GLU C 501 " pdb=" CG GLU C 501 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB ASP C 185 " pdb=" CG ASP C 185 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.31e-01 bond pdb=" N PRO C 481 " pdb=" CA PRO C 481 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.80e-01 bond pdb=" CB ASP B 34 " pdb=" CG ASP B 34 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.81e-01 ... (remaining 5211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 7096 4.93 - 9.87: 1 9.87 - 14.80: 1 14.80 - 19.74: 1 19.74 - 24.67: 1 Bond angle restraints: 7100 Sorted by residual: angle pdb=" O GLN B 45 " pdb=" C GLN B 45 " pdb=" N ARG B 46 " ideal model delta sigma weight residual 121.74 97.07 24.67 1.31e+00 5.83e-01 3.55e+02 angle pdb=" CA GLN B 45 " pdb=" C GLN B 45 " pdb=" N ARG B 46 " ideal model delta sigma weight residual 116.50 133.61 -17.11 1.63e+00 3.76e-01 1.10e+02 angle pdb=" C GLN B 45 " pdb=" N ARG B 46 " pdb=" CA ARG B 46 " ideal model delta sigma weight residual 122.77 134.75 -11.98 1.33e+00 5.65e-01 8.12e+01 angle pdb=" CA GLU C 501 " pdb=" CB GLU C 501 " pdb=" CG GLU C 501 " ideal model delta sigma weight residual 114.10 118.75 -4.65 2.00e+00 2.50e-01 5.40e+00 angle pdb=" N LYS C 32 " pdb=" CA LYS C 32 " pdb=" C LYS C 32 " ideal model delta sigma weight residual 110.30 113.59 -3.29 1.50e+00 4.44e-01 4.82e+00 ... (remaining 7095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2733 17.99 - 35.98: 298 35.98 - 53.98: 69 53.98 - 71.97: 16 71.97 - 89.96: 6 Dihedral angle restraints: 3122 sinusoidal: 1197 harmonic: 1925 Sorted by residual: dihedral pdb=" CB CYS C 199 " pdb=" SG CYS C 199 " pdb=" SG CYS C 212 " pdb=" CB CYS C 212 " ideal model delta sinusoidal sigma weight residual -86.00 -156.23 70.23 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.10 43.90 1 1.00e+01 1.00e-02 2.68e+01 dihedral pdb=" CB CYS C 224 " pdb=" SG CYS C 224 " pdb=" SG CYS C 235 " pdb=" CB CYS C 235 " ideal model delta sinusoidal sigma weight residual -86.00 -48.52 -37.48 1 1.00e+01 1.00e-02 1.98e+01 ... (remaining 3119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 447 0.027 - 0.053: 235 0.053 - 0.080: 59 0.080 - 0.106: 50 0.106 - 0.133: 19 Chirality restraints: 810 Sorted by residual: chirality pdb=" CA VAL C 116 " pdb=" N VAL C 116 " pdb=" C VAL C 116 " pdb=" CB VAL C 116 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE C 435 " pdb=" N ILE C 435 " pdb=" C ILE C 435 " pdb=" CB ILE C 435 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE C 86 " pdb=" N ILE C 86 " pdb=" C ILE C 86 " pdb=" CB ILE C 86 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 807 not shown) Planarity restraints: 919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 45 " -0.060 2.00e-02 2.50e+03 9.97e-02 9.94e+01 pdb=" C GLN B 45 " 0.173 2.00e-02 2.50e+03 pdb=" O GLN B 45 " -0.051 2.00e-02 2.50e+03 pdb=" N ARG B 46 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 377 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO C 378 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 378 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 378 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 299 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO C 300 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 300 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 300 " -0.018 5.00e-02 4.00e+02 ... (remaining 916 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 493 2.75 - 3.29: 4453 3.29 - 3.83: 8201 3.83 - 4.36: 10295 4.36 - 4.90: 17828 Nonbonded interactions: 41270 Sorted by model distance: nonbonded pdb=" OH TYR C 163 " pdb=" O HIS C 193 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR C 166 " pdb=" O SER C 202 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLN C 164 " pdb=" NH1 ARG C 188 " model vdw 2.289 3.120 nonbonded pdb=" O GLY A 42 " pdb=" OG1 THR C 67 " model vdw 2.304 3.040 nonbonded pdb=" N GLU C 501 " pdb=" OE1 GLU C 501 " model vdw 2.312 3.120 ... (remaining 41265 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: 1.120 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.170 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 : 0.002 0.038 5232 Z= 0.093 Angle : 0.606 24.670 7132 Z= 0.376 Chirality : 0.042 0.133 810 Planarity : 0.004 0.100 919 Dihedral : 16.069 89.960 1840 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.57 % Allowed : 16.18 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.33), residues: 659 helix: -1.09 (1.35), residues: 17 sheet: 0.53 (0.46), residues: 143 loop : 0.01 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 330 TYR 0.009 0.001 TYR B 97 PHE 0.006 0.001 PHE B 32 TRP 0.006 0.001 TRP C 452 HIS 0.004 0.001 HIS C 469 Details of bonding type rmsd covalent geometry : bond 0.00184 ( 5216) covalent geometry : angle 0.60612 ( 7100) SS BOND : bond 0.00193 ( 16) SS BOND : angle 0.48133 ( 32) hydrogen bonds : bond 0.25011 ( 132) hydrogen bonds : angle 8.96957 ( 330) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 14 residues processed: 77 average time/residue: 0.3661 time to fit residues: 29.8023 Evaluate side-chains 75 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 432 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 HIS C 193 HIS C 213 GLN C 319 ASN C 349 HIS C 469 HIS C 470 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.110267 restraints weight = 5058.786| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.66 r_work: 0.3105 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5232 Z= 0.180 Angle : 0.633 6.958 7132 Z= 0.330 Chirality : 0.046 0.150 810 Planarity : 0.004 0.038 919 Dihedral : 6.982 52.882 751 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.12 % Allowed : 15.44 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.33), residues: 659 helix: -2.04 (1.05), residues: 23 sheet: 0.25 (0.40), residues: 161 loop : -0.06 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 70 TYR 0.010 0.002 TYR B 97 PHE 0.016 0.002 PHE B 32 TRP 0.010 0.002 TRP C 169 HIS 0.011 0.002 HIS C 469 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 5216) covalent geometry : angle 0.62999 ( 7100) SS BOND : bond 0.00447 ( 16) SS BOND : angle 1.09269 ( 32) hydrogen bonds : bond 0.04834 ( 132) hydrogen bonds : angle 5.78012 ( 330) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.114 Fit side-chains REVERT: C 398 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8029 (mm-40) outliers start: 17 outliers final: 8 residues processed: 71 average time/residue: 0.3877 time to fit residues: 28.8335 Evaluate side-chains 66 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 398 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 19 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.141875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108818 restraints weight = 5020.833| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.66 r_work: 0.3070 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5232 Z= 0.187 Angle : 0.644 7.426 7132 Z= 0.336 Chirality : 0.047 0.149 810 Planarity : 0.004 0.036 919 Dihedral : 6.641 59.168 734 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.23 % Allowed : 16.36 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.33), residues: 659 helix: -2.13 (1.03), residues: 23 sheet: 0.14 (0.38), residues: 161 loop : -0.13 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 39 TYR 0.011 0.002 TYR A 93 PHE 0.015 0.002 PHE B 32 TRP 0.013 0.002 TRP C 169 HIS 0.008 0.002 HIS C 469 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 5216) covalent geometry : angle 0.64156 ( 7100) SS BOND : bond 0.00379 ( 16) SS BOND : angle 1.10522 ( 32) hydrogen bonds : bond 0.04307 ( 132) hydrogen bonds : angle 5.32159 ( 330) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: C 398 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8030 (mm-40) REVERT: C 501 GLU cc_start: 0.7325 (mp0) cc_final: 0.7019 (mp0) outliers start: 23 outliers final: 13 residues processed: 76 average time/residue: 0.3180 time to fit residues: 25.5557 Evaluate side-chains 69 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 398 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.110331 restraints weight = 5066.340| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.68 r_work: 0.3101 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5232 Z= 0.126 Angle : 0.564 6.694 7132 Z= 0.297 Chirality : 0.044 0.143 810 Planarity : 0.004 0.033 919 Dihedral : 6.146 57.559 732 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.86 % Allowed : 16.54 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.33), residues: 659 helix: -2.03 (1.05), residues: 23 sheet: 0.21 (0.38), residues: 161 loop : -0.10 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 487 TYR 0.009 0.001 TYR B 97 PHE 0.011 0.001 PHE B 32 TRP 0.009 0.001 TRP B 110 HIS 0.003 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5216) covalent geometry : angle 0.56202 ( 7100) SS BOND : bond 0.00282 ( 16) SS BOND : angle 0.89332 ( 32) hydrogen bonds : bond 0.03393 ( 132) hydrogen bonds : angle 4.95986 ( 330) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: C 398 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8040 (mm-40) REVERT: C 501 GLU cc_start: 0.7377 (mp0) cc_final: 0.6981 (mp0) outliers start: 21 outliers final: 11 residues processed: 76 average time/residue: 0.3672 time to fit residues: 29.2876 Evaluate side-chains 70 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 398 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 HIS C 193 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.142754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109998 restraints weight = 5156.028| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.68 r_work: 0.3084 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5232 Z= 0.122 Angle : 0.560 6.652 7132 Z= 0.294 Chirality : 0.044 0.143 810 Planarity : 0.004 0.035 919 Dihedral : 5.156 48.393 729 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.86 % Allowed : 16.36 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.33), residues: 659 helix: -1.96 (1.05), residues: 23 sheet: 0.47 (0.39), residues: 154 loop : -0.16 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 487 TYR 0.009 0.001 TYR B 97 PHE 0.010 0.001 PHE B 32 TRP 0.008 0.001 TRP C 169 HIS 0.003 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5216) covalent geometry : angle 0.55787 ( 7100) SS BOND : bond 0.00277 ( 16) SS BOND : angle 0.86211 ( 32) hydrogen bonds : bond 0.03248 ( 132) hydrogen bonds : angle 4.81328 ( 330) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: B 14 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6856 (tp40) REVERT: C 398 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8032 (mm-40) REVERT: C 459 ARG cc_start: 0.7509 (mtm110) cc_final: 0.7284 (mtm110) REVERT: C 501 GLU cc_start: 0.7351 (mp0) cc_final: 0.6967 (mp0) outliers start: 21 outliers final: 12 residues processed: 78 average time/residue: 0.3822 time to fit residues: 31.1682 Evaluate side-chains 74 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 398 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 57 optimal weight: 0.0770 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.107896 restraints weight = 5114.116| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.67 r_work: 0.3041 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5232 Z= 0.262 Angle : 0.725 7.407 7132 Z= 0.376 Chirality : 0.050 0.152 810 Planarity : 0.005 0.039 919 Dihedral : 5.799 55.515 729 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.86 % Allowed : 16.91 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.32), residues: 659 helix: -2.09 (1.02), residues: 23 sheet: 0.08 (0.37), residues: 161 loop : -0.29 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 226 TYR 0.016 0.002 TYR A 93 PHE 0.014 0.002 PHE B 32 TRP 0.017 0.003 TRP C 169 HIS 0.006 0.002 HIS C 490 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 5216) covalent geometry : angle 0.71965 ( 7100) SS BOND : bond 0.00492 ( 16) SS BOND : angle 1.54751 ( 32) hydrogen bonds : bond 0.04498 ( 132) hydrogen bonds : angle 5.17068 ( 330) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: C 398 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8017 (mm-40) REVERT: C 501 GLU cc_start: 0.7372 (mp0) cc_final: 0.6955 (mp0) outliers start: 21 outliers final: 13 residues processed: 72 average time/residue: 0.4456 time to fit residues: 33.7090 Evaluate side-chains 66 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 398 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 15 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN C 349 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111870 restraints weight = 5031.632| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.66 r_work: 0.3090 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5232 Z= 0.106 Angle : 0.543 6.835 7132 Z= 0.287 Chirality : 0.044 0.138 810 Planarity : 0.003 0.032 919 Dihedral : 5.162 46.666 729 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.49 % Allowed : 16.73 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.32), residues: 659 helix: -1.95 (1.03), residues: 23 sheet: 0.35 (0.38), residues: 154 loop : -0.19 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 487 TYR 0.009 0.001 TYR B 97 PHE 0.009 0.001 PHE B 32 TRP 0.009 0.001 TRP B 110 HIS 0.011 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 5216) covalent geometry : angle 0.54128 ( 7100) SS BOND : bond 0.00261 ( 16) SS BOND : angle 0.86532 ( 32) hydrogen bonds : bond 0.03011 ( 132) hydrogen bonds : angle 4.77576 ( 330) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: C 398 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8059 (mm-40) REVERT: C 459 ARG cc_start: 0.7571 (mtm110) cc_final: 0.7333 (mtm110) REVERT: C 501 GLU cc_start: 0.7355 (mp0) cc_final: 0.6991 (mp0) outliers start: 19 outliers final: 11 residues processed: 74 average time/residue: 0.4511 time to fit residues: 34.9830 Evaluate side-chains 69 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 398 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 53 optimal weight: 0.0670 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN C 349 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.110510 restraints weight = 5086.616| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.67 r_work: 0.3115 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5232 Z= 0.109 Angle : 0.551 6.158 7132 Z= 0.290 Chirality : 0.044 0.141 810 Planarity : 0.003 0.033 919 Dihedral : 5.083 47.788 729 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.94 % Allowed : 17.65 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.33), residues: 659 helix: -1.89 (1.04), residues: 23 sheet: 0.44 (0.39), residues: 154 loop : -0.14 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 487 TYR 0.009 0.001 TYR B 97 PHE 0.009 0.001 PHE B 32 TRP 0.008 0.001 TRP C 169 HIS 0.013 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5216) covalent geometry : angle 0.54672 ( 7100) SS BOND : bond 0.00270 ( 16) SS BOND : angle 1.18715 ( 32) hydrogen bonds : bond 0.03003 ( 132) hydrogen bonds : angle 4.68236 ( 330) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: C 286 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7077 (pt0) REVERT: C 398 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8039 (mm-40) REVERT: C 459 ARG cc_start: 0.7544 (mtm110) cc_final: 0.7301 (mtm110) REVERT: C 501 GLU cc_start: 0.7398 (mp0) cc_final: 0.6971 (mp0) outliers start: 16 outliers final: 10 residues processed: 69 average time/residue: 0.4218 time to fit residues: 30.4657 Evaluate side-chains 66 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 398 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 4 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 18 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN C 349 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.111886 restraints weight = 5079.104| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.67 r_work: 0.3113 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5232 Z= 0.097 Angle : 0.528 6.230 7132 Z= 0.278 Chirality : 0.043 0.137 810 Planarity : 0.003 0.032 919 Dihedral : 4.928 45.958 729 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.57 % Allowed : 18.20 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.33), residues: 659 helix: -1.87 (1.02), residues: 23 sheet: 0.50 (0.38), residues: 154 loop : -0.11 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.009 0.001 TYR B 97 PHE 0.008 0.001 PHE B 32 TRP 0.008 0.001 TRP B 110 HIS 0.012 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 5216) covalent geometry : angle 0.52709 ( 7100) SS BOND : bond 0.00225 ( 16) SS BOND : angle 0.77174 ( 32) hydrogen bonds : bond 0.02771 ( 132) hydrogen bonds : angle 4.58687 ( 330) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: B 14 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6819 (tp40) REVERT: C 286 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7075 (pt0) REVERT: C 398 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8025 (mm-40) REVERT: C 459 ARG cc_start: 0.7479 (mtm110) cc_final: 0.7255 (mtm110) REVERT: C 501 GLU cc_start: 0.7336 (mp0) cc_final: 0.6917 (mp0) outliers start: 14 outliers final: 8 residues processed: 68 average time/residue: 0.3966 time to fit residues: 28.1264 Evaluate side-chains 66 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 398 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 14 optimal weight: 0.8980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 HIS C 193 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN C 349 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110952 restraints weight = 5134.138| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.70 r_work: 0.3125 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5232 Z= 0.110 Angle : 0.545 5.903 7132 Z= 0.286 Chirality : 0.044 0.141 810 Planarity : 0.003 0.034 919 Dihedral : 4.934 48.285 728 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.57 % Allowed : 18.20 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.33), residues: 659 helix: -1.89 (1.01), residues: 23 sheet: 0.50 (0.38), residues: 154 loop : -0.11 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.009 0.001 TYR B 97 PHE 0.009 0.001 PHE B 32 TRP 0.008 0.001 TRP C 169 HIS 0.011 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 5216) covalent geometry : angle 0.54345 ( 7100) SS BOND : bond 0.00262 ( 16) SS BOND : angle 0.85655 ( 32) hydrogen bonds : bond 0.02963 ( 132) hydrogen bonds : angle 4.58846 ( 330) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: B 14 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6811 (tp40) REVERT: C 286 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7076 (pt0) REVERT: C 398 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8023 (mm-40) REVERT: C 459 ARG cc_start: 0.7487 (mtm110) cc_final: 0.7250 (mtm110) REVERT: C 501 GLU cc_start: 0.7307 (mp0) cc_final: 0.6890 (mp0) outliers start: 14 outliers final: 9 residues processed: 68 average time/residue: 0.4344 time to fit residues: 30.8271 Evaluate side-chains 67 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 192 CYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 398 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN C 349 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.145630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112870 restraints weight = 5129.460| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.69 r_work: 0.3120 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5232 Z= 0.090 Angle : 0.513 5.949 7132 Z= 0.270 Chirality : 0.043 0.136 810 Planarity : 0.003 0.033 919 Dihedral : 4.761 45.068 728 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.39 % Allowed : 18.38 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.33), residues: 659 helix: -1.77 (1.05), residues: 23 sheet: 0.55 (0.38), residues: 154 loop : -0.08 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 70 TYR 0.008 0.001 TYR B 97 PHE 0.007 0.001 PHE B 32 TRP 0.008 0.001 TRP B 110 HIS 0.012 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 5216) covalent geometry : angle 0.51221 ( 7100) SS BOND : bond 0.00208 ( 16) SS BOND : angle 0.70096 ( 32) hydrogen bonds : bond 0.02628 ( 132) hydrogen bonds : angle 4.51468 ( 330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1645.41 seconds wall clock time: 28 minutes 44.03 seconds (1724.03 seconds total)