Starting phenix.real_space_refine on Tue Feb 3 17:42:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kkw_62396/02_2026/9kkw_62396.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kkw_62396/02_2026/9kkw_62396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kkw_62396/02_2026/9kkw_62396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kkw_62396/02_2026/9kkw_62396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kkw_62396/02_2026/9kkw_62396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kkw_62396/02_2026/9kkw_62396.map" } resolution = 2.92 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= 0.002 sd= 0.176 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 35 5.16 5 C 3638 2.51 5 N 958 2.21 5 O 981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 5612 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4330 Classifications: {'peptide': 565} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 186 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 575 Classifications: {'peptide': 117} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 107} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'UNK:plan-1': 117} Unresolved non-hydrogen planarities: 117 Chain: "L" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 521 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 9, 'truncation_to_alanine': 97} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Time building chain proxies: 1.50, per 1000 atoms: 0.27 Number of scatterers: 5612 At special positions: 0 Unit cell: (113.102, 99.231, 80.025, 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 35 16.00 O 981 8.00 N 958 7.00 C 3638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.02 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " 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 294.6 milliseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 86.1% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 22 through 45 removed outlier: 3.987A pdb=" N VAL A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 95 through 113 removed outlier: 4.070A pdb=" N GLU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TRP A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 136 through 154 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 173 through 191 Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.824A pdb=" N THR A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.604A pdb=" N VAL A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.970A pdb=" N TYR A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 294 removed outlier: 4.231A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.621A pdb=" N ALA A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 5.018A pdb=" N MET A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 375 through 409 removed outlier: 4.164A pdb=" N GLY A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 418 through 447 Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 463 through 477 removed outlier: 4.485A pdb=" N VAL A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 507 removed outlier: 4.015A pdb=" N ARG A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) Proline residue: A 502 - end of helix Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 525 through 546 Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.806A pdb=" N ARG A 564 " --> pdb=" O PHE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 671 Processing helix chain 'B' and resid 29 through 52 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 101 through 104 removed outlier: 3.783A pdb=" N UNK H 104 " --> pdb=" O UNK H 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 101 through 104' Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.650A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N UNK H 33 " --> pdb=" O UNK H 99 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N UNK H 108 " --> pdb=" O UNK H 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.650A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N UNK H 33 " --> pdb=" O UNK H 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.573A pdb=" N UNK L 72 " --> pdb=" O UNK L 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.445A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1143 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: 0.98 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 896 1.31 - 1.43: 1528 1.43 - 1.56: 3253 1.56 - 1.69: 0 1.69 - 1.82: 54 Bond restraints: 5731 Sorted by residual: bond pdb=" C TYR A 32 " pdb=" O TYR A 32 " ideal model delta sigma weight residual 1.237 1.177 0.059 1.19e-02 7.06e+03 2.49e+01 bond pdb=" CA TYR A 32 " pdb=" C TYR A 32 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.29e-02 6.01e+03 6.90e+00 bond pdb=" CB TYR A 32 " pdb=" CG TYR A 32 " ideal model delta sigma weight residual 1.512 1.455 0.057 2.20e-02 2.07e+03 6.78e+00 bond pdb=" C TYR A 32 " pdb=" N PHE A 33 " ideal model delta sigma weight residual 1.335 1.303 0.031 1.36e-02 5.41e+03 5.35e+00 bond pdb=" CA TYR A 32 " pdb=" CB TYR A 32 " ideal model delta sigma weight residual 1.528 1.495 0.033 1.59e-02 3.96e+03 4.28e+00 ... (remaining 5726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 7494 1.61 - 3.22: 292 3.22 - 4.84: 48 4.84 - 6.45: 6 6.45 - 8.06: 3 Bond angle restraints: 7843 Sorted by residual: angle pdb=" C UNK L 56 " pdb=" N UNK L 57 " pdb=" CA UNK L 57 " ideal model delta sigma weight residual 121.70 126.97 -5.27 1.80e+00 3.09e-01 8.56e+00 angle pdb=" CA PRO A 324 " pdb=" N PRO A 324 " pdb=" CD PRO A 324 " ideal model delta sigma weight residual 112.00 107.91 4.09 1.40e+00 5.10e-01 8.55e+00 angle pdb=" C UNK L 15 " pdb=" N UNK L 16 " pdb=" CA UNK L 16 " ideal model delta sigma weight residual 121.70 126.40 -4.70 1.80e+00 3.09e-01 6.81e+00 angle pdb=" CA PRO A 324 " pdb=" CB PRO A 324 " pdb=" CG PRO A 324 " ideal model delta sigma weight residual 104.50 99.75 4.75 1.90e+00 2.77e-01 6.24e+00 angle pdb=" CB PRO A 324 " pdb=" CG PRO A 324 " pdb=" CD PRO A 324 " ideal model delta sigma weight residual 106.10 98.36 7.74 3.20e+00 9.77e-02 5.86e+00 ... (remaining 7838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 2942 17.70 - 35.40: 259 35.40 - 53.11: 81 53.11 - 70.81: 17 70.81 - 88.51: 2 Dihedral angle restraints: 3301 sinusoidal: 991 harmonic: 2310 Sorted by residual: dihedral pdb=" CA CYS A 355 " pdb=" C CYS A 355 " pdb=" N GLY A 356 " pdb=" CA GLY A 356 " ideal model delta harmonic sigma weight residual 180.00 -158.49 -21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -119.99 33.99 1 1.00e+01 1.00e-02 1.64e+01 dihedral pdb=" CA VAL A 203 " pdb=" C VAL A 203 " pdb=" N GLN A 204 " pdb=" CA GLN A 204 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 3298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 772 0.048 - 0.096: 149 0.096 - 0.143: 20 0.143 - 0.191: 2 0.191 - 0.239: 1 Chirality restraints: 944 Sorted by residual: chirality pdb=" CB ILE A 433 " pdb=" CA ILE A 433 " pdb=" CG1 ILE A 433 " pdb=" CG2 ILE A 433 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE A 297 " pdb=" CA ILE A 297 " pdb=" CG1 ILE A 297 " pdb=" CG2 ILE A 297 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA ILE A 551 " pdb=" N ILE A 551 " pdb=" C ILE A 551 " pdb=" CB ILE A 551 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 941 not shown) Planarity restraints: 996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 464 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO A 465 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 465 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 465 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 206 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C PHE A 206 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE A 206 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 207 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 284 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C THR A 284 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A 284 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 285 " -0.012 2.00e-02 2.50e+03 ... (remaining 993 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1693 2.81 - 3.34: 5461 3.34 - 3.86: 9374 3.86 - 4.38: 10389 4.38 - 4.90: 18167 Nonbonded interactions: 45084 Sorted by model distance: nonbonded pdb=" O THR A 271 " pdb=" OG1 THR A 271 " model vdw 2.292 3.040 nonbonded pdb=" OD1 ASN A 75 " pdb=" NZ LYS A 321 " model vdw 2.314 3.120 nonbonded pdb=" O PHE A 230 " pdb=" OH TYR A 263 " model vdw 2.342 3.040 nonbonded pdb=" O PHE A 561 " pdb=" NE ARG A 564 " model vdw 2.349 3.120 nonbonded pdb=" OH TYR A 226 " pdb=" OH TYR A 671 " model vdw 2.351 3.040 ... (remaining 45079 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 Found NCS groups: ncs_group { reference = (chain 'H' and (resid 12 through 26 or (resid 27 and (name N or name CA or name \ C or name O )) or resid 28 through 51 or (resid 52 and (name N or name CA or nam \ e C or name O )) or resid 53 through 67 or (resid 68 and (name N or name CA or n \ ame C or name O )) or resid 69 through 74 or (resid 75 and (name N or name CA or \ name C or name O )) or resid 76 or (resid 77 and (name N or name CA or name C o \ r name O )) or resid 78 or (resid 79 and (name N or name CA or name C or name O \ )) or resid 80 through 110 or (resid 111 through 112 and (name N or name CA or n \ ame C or name O )) or resid 113 through 117)) selection = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O )) or resid 5 through 14 or (resid 15 through 16 and (name N or name CA \ or name C or name O )) or resid 17 through 37 or (resid 38 and (name N or name \ CA or name C or name O )) or resid 39 through 54 or (resid 55 and (name N or nam \ e CA or name C or name O )) or resid 56 through 87 or (resid 88 through 89 and ( \ name N or name CA or name C or name O )) or resid 90 or (resid 91 and (name N or \ name CA or name C or name O )) or resid 92 through 106)) } 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: 1.230 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.640 Find NCS groups from input model: 0.040 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:8.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 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 : 0.004 0.059 5735 Z= 0.183 Angle : 0.732 8.060 7851 Z= 0.359 Chirality : 0.038 0.239 944 Planarity : 0.005 0.059 996 Dihedral : 15.769 88.512 1809 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.73 % Allowed : 28.72 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.37), residues: 582 helix: 1.25 (0.27), residues: 440 sheet: None (None), residues: 0 loop : -1.10 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 257 TYR 0.017 0.002 TYR A 319 PHE 0.012 0.001 PHE A 206 TRP 0.019 0.001 TRP A 291 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5731) covalent geometry : angle 0.73148 ( 7843) SS BOND : bond 0.00803 ( 4) SS BOND : angle 1.19693 ( 8) hydrogen bonds : bond 0.12854 ( 389) hydrogen bonds : angle 6.36248 ( 1143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 VAL cc_start: 0.8155 (t) cc_final: 0.7922 (m) REVERT: A 325 MET cc_start: 0.8493 (tpp) cc_final: 0.8237 (tpp) REVERT: A 425 VAL cc_start: 0.7804 (t) cc_final: 0.7479 (t) outliers start: 13 outliers final: 9 residues processed: 95 average time/residue: 0.5290 time to fit residues: 52.7995 Evaluate side-chains 88 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 475 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 483 GLN A 565 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.186047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137084 restraints weight = 6244.066| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.11 r_work: 0.3403 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 5735 Z= 0.259 Angle : 0.772 8.932 7851 Z= 0.369 Chirality : 0.045 0.194 944 Planarity : 0.006 0.062 996 Dihedral : 5.944 48.520 869 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.56 % Rotamer: Outliers : 9.85 % Allowed : 21.38 % Favored : 68.76 % 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: 0.74 (0.36), residues: 582 helix: 1.04 (0.25), residues: 441 sheet: None (None), residues: 0 loop : -1.12 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.015 0.002 TYR A 410 PHE 0.021 0.002 PHE A 230 TRP 0.022 0.002 TRP A 291 HIS 0.003 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 5731) covalent geometry : angle 0.76876 ( 7843) SS BOND : bond 0.00669 ( 4) SS BOND : angle 2.49845 ( 8) hydrogen bonds : bond 0.04093 ( 389) hydrogen bonds : angle 5.26115 ( 1143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 78 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.6320 (OUTLIER) cc_final: 0.5860 (m-30) REVERT: A 76 ILE cc_start: 0.6713 (mt) cc_final: 0.6494 (mt) REVERT: A 139 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6870 (ttm-80) REVERT: A 154 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7310 (ttmm) REVERT: A 222 GLU cc_start: 0.7933 (tp30) cc_final: 0.7477 (tp30) REVERT: A 412 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7231 (mtm110) outliers start: 47 outliers final: 17 residues processed: 112 average time/residue: 0.4421 time to fit residues: 52.2327 Evaluate side-chains 92 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 495 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.191935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147759 restraints weight = 6259.318| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.85 r_work: 0.3374 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5735 Z= 0.133 Angle : 0.620 9.231 7851 Z= 0.293 Chirality : 0.039 0.184 944 Planarity : 0.005 0.056 996 Dihedral : 4.963 52.901 862 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 7.76 % Allowed : 24.11 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.37), residues: 582 helix: 1.49 (0.26), residues: 435 sheet: None (None), residues: 0 loop : -0.67 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.012 0.001 TYR A 410 PHE 0.014 0.001 PHE A 534 TRP 0.016 0.001 TRP A 291 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5731) covalent geometry : angle 0.61954 ( 7843) SS BOND : bond 0.00759 ( 4) SS BOND : angle 1.01274 ( 8) hydrogen bonds : bond 0.03342 ( 389) hydrogen bonds : angle 4.82484 ( 1143) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7352 (ttm-80) REVERT: A 154 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7869 (ttmm) REVERT: A 198 MET cc_start: 0.7790 (mmt) cc_final: 0.7202 (tpt) REVERT: A 222 GLU cc_start: 0.8051 (tp30) cc_final: 0.7714 (tp30) REVERT: A 412 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7364 (mtm110) REVERT: A 420 ARG cc_start: 0.6228 (ttt180) cc_final: 0.5439 (ppt90) REVERT: A 425 VAL cc_start: 0.8146 (t) cc_final: 0.7836 (t) REVERT: B 40 PHE cc_start: 0.5836 (OUTLIER) cc_final: 0.5134 (t80) outliers start: 37 outliers final: 11 residues processed: 115 average time/residue: 0.4557 time to fit residues: 55.3626 Evaluate side-chains 99 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 40 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 5 optimal weight: 0.4980 chunk 53 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.190777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146552 restraints weight = 6314.235| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.85 r_work: 0.3358 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5735 Z= 0.152 Angle : 0.636 9.616 7851 Z= 0.299 Chirality : 0.039 0.194 944 Planarity : 0.005 0.055 996 Dihedral : 4.816 55.787 859 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.56 % Rotamer: Outliers : 7.34 % Allowed : 25.79 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.36), residues: 582 helix: 1.54 (0.26), residues: 431 sheet: None (None), residues: 0 loop : -0.70 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 132 TYR 0.013 0.002 TYR A 410 PHE 0.015 0.001 PHE A 230 TRP 0.015 0.001 TRP A 291 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5731) covalent geometry : angle 0.63557 ( 7843) SS BOND : bond 0.01003 ( 4) SS BOND : angle 1.11639 ( 8) hydrogen bonds : bond 0.03359 ( 389) hydrogen bonds : angle 4.77171 ( 1143) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.5697 (ttp80) REVERT: A 139 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7352 (ttm-80) REVERT: A 154 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7904 (ttmm) REVERT: A 198 MET cc_start: 0.7739 (mmt) cc_final: 0.6722 (pmm) REVERT: A 412 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7365 (mtm110) REVERT: A 420 ARG cc_start: 0.6248 (ttt180) cc_final: 0.5456 (ppt90) REVERT: B 40 PHE cc_start: 0.5637 (OUTLIER) cc_final: 0.5149 (t80) outliers start: 35 outliers final: 16 residues processed: 105 average time/residue: 0.4537 time to fit residues: 50.3447 Evaluate side-chains 95 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 40 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 23 optimal weight: 0.0670 chunk 60 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.189089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.142564 restraints weight = 6417.362| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.96 r_work: 0.3328 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5735 Z= 0.182 Angle : 0.665 9.539 7851 Z= 0.313 Chirality : 0.040 0.213 944 Planarity : 0.005 0.057 996 Dihedral : 4.810 58.964 858 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 9.01 % Allowed : 24.74 % Favored : 66.25 % 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: 1.38 (0.36), residues: 582 helix: 1.49 (0.25), residues: 431 sheet: None (None), residues: 0 loop : -0.66 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.017 0.002 TYR A 410 PHE 0.017 0.001 PHE A 534 TRP 0.017 0.001 TRP A 291 HIS 0.002 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 5731) covalent geometry : angle 0.66467 ( 7843) SS BOND : bond 0.00981 ( 4) SS BOND : angle 1.18954 ( 8) hydrogen bonds : bond 0.03493 ( 389) hydrogen bonds : angle 4.83366 ( 1143) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 79 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.5549 (ttp80) REVERT: A 139 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7298 (ttm-80) REVERT: A 154 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7837 (ttmm) REVERT: A 198 MET cc_start: 0.7678 (mmt) cc_final: 0.6576 (pmm) REVERT: A 412 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7230 (mtm110) REVERT: A 420 ARG cc_start: 0.6242 (ttt180) cc_final: 0.5428 (ppt90) REVERT: A 425 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7801 (t) REVERT: B 40 PHE cc_start: 0.5694 (OUTLIER) cc_final: 0.5067 (t80) outliers start: 43 outliers final: 20 residues processed: 111 average time/residue: 0.4546 time to fit residues: 53.4161 Evaluate side-chains 100 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 40 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.189426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146452 restraints weight = 6361.268| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.72 r_work: 0.3351 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5735 Z= 0.181 Angle : 0.676 10.606 7851 Z= 0.316 Chirality : 0.041 0.223 944 Planarity : 0.005 0.057 996 Dihedral : 4.828 59.894 858 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 8.18 % Allowed : 26.21 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.36), residues: 582 helix: 1.50 (0.25), residues: 431 sheet: None (None), residues: 0 loop : -0.66 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 352 TYR 0.017 0.002 TYR A 410 PHE 0.017 0.001 PHE A 534 TRP 0.017 0.001 TRP A 291 HIS 0.002 0.000 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 5731) covalent geometry : angle 0.67514 ( 7843) SS BOND : bond 0.01011 ( 4) SS BOND : angle 1.38563 ( 8) hydrogen bonds : bond 0.03470 ( 389) hydrogen bonds : angle 4.82171 ( 1143) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 79 time to evaluate : 0.180 Fit side-chains REVERT: A 132 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.5620 (ttp80) REVERT: A 137 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.8005 (ptp-170) REVERT: A 139 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7381 (ttm-80) REVERT: A 198 MET cc_start: 0.7630 (mmt) cc_final: 0.6552 (pmm) REVERT: A 412 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7099 (mtm110) REVERT: A 420 ARG cc_start: 0.6284 (ttt180) cc_final: 0.5481 (ppt90) REVERT: A 425 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.7965 (t) REVERT: B 40 PHE cc_start: 0.5801 (OUTLIER) cc_final: 0.5172 (t80) outliers start: 39 outliers final: 22 residues processed: 107 average time/residue: 0.5014 time to fit residues: 56.5762 Evaluate side-chains 107 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 40 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.189330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145020 restraints weight = 6480.262| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.86 r_work: 0.3388 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5735 Z= 0.172 Angle : 0.682 10.713 7851 Z= 0.318 Chirality : 0.040 0.247 944 Planarity : 0.005 0.058 996 Dihedral : 4.779 57.971 858 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 7.13 % Allowed : 26.62 % Favored : 66.25 % 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: 1.35 (0.36), residues: 582 helix: 1.46 (0.25), residues: 431 sheet: None (None), residues: 0 loop : -0.67 (0.56), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 352 TYR 0.018 0.002 TYR A 410 PHE 0.017 0.001 PHE A 534 TRP 0.017 0.001 TRP A 291 HIS 0.002 0.000 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 5731) covalent geometry : angle 0.67896 ( 7843) SS BOND : bond 0.00881 ( 4) SS BOND : angle 2.08072 ( 8) hydrogen bonds : bond 0.03437 ( 389) hydrogen bonds : angle 4.80550 ( 1143) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.5642 (ttp80) REVERT: A 139 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7407 (ttm-80) REVERT: A 154 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7927 (mtmm) REVERT: A 198 MET cc_start: 0.7673 (mmt) cc_final: 0.6514 (pmm) REVERT: A 412 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7132 (mtm110) REVERT: A 420 ARG cc_start: 0.6317 (ttt180) cc_final: 0.5530 (ppt90) REVERT: A 425 VAL cc_start: 0.8327 (t) cc_final: 0.8016 (t) REVERT: B 40 PHE cc_start: 0.5879 (OUTLIER) cc_final: 0.5246 (t80) outliers start: 34 outliers final: 23 residues processed: 105 average time/residue: 0.4898 time to fit residues: 54.1236 Evaluate side-chains 107 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 40 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 0.0770 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 0.0470 chunk 74 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.192165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146623 restraints weight = 6344.715| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.95 r_work: 0.3377 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5735 Z= 0.122 Angle : 0.624 10.257 7851 Z= 0.291 Chirality : 0.038 0.255 944 Planarity : 0.005 0.054 996 Dihedral : 4.498 55.761 857 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.09 % Favored : 96.74 % Rotamer: Outliers : 5.45 % Allowed : 28.30 % Favored : 66.25 % 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: 1.72 (0.37), residues: 582 helix: 1.71 (0.26), residues: 433 sheet: None (None), residues: 0 loop : -0.47 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 352 TYR 0.017 0.001 TYR A 410 PHE 0.015 0.001 PHE A 230 TRP 0.014 0.001 TRP A 291 HIS 0.001 0.000 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 5731) covalent geometry : angle 0.62263 ( 7843) SS BOND : bond 0.00680 ( 4) SS BOND : angle 1.61428 ( 8) hydrogen bonds : bond 0.03076 ( 389) hydrogen bonds : angle 4.57013 ( 1143) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.4836 (OUTLIER) cc_final: 0.3686 (p-90) REVERT: A 139 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7240 (ttm-80) REVERT: A 154 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7782 (mtmm) REVERT: A 198 MET cc_start: 0.7664 (mmt) cc_final: 0.6995 (tpt) REVERT: A 412 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7138 (mtm110) REVERT: A 420 ARG cc_start: 0.6160 (ttt180) cc_final: 0.5360 (ppt90) REVERT: B 40 PHE cc_start: 0.5604 (OUTLIER) cc_final: 0.5119 (t80) outliers start: 26 outliers final: 12 residues processed: 102 average time/residue: 0.4834 time to fit residues: 51.9165 Evaluate side-chains 96 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 40 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 60 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.190235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144303 restraints weight = 6385.917| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.95 r_work: 0.3353 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5735 Z= 0.157 Angle : 0.659 9.709 7851 Z= 0.309 Chirality : 0.039 0.269 944 Planarity : 0.005 0.055 996 Dihedral : 4.604 54.392 857 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.56 % Rotamer: Outliers : 4.82 % Allowed : 29.56 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.36), residues: 582 helix: 1.65 (0.25), residues: 433 sheet: None (None), residues: 0 loop : -0.51 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 352 TYR 0.019 0.002 TYR A 410 PHE 0.016 0.001 PHE A 534 TRP 0.013 0.001 TRP A 291 HIS 0.002 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 5731) covalent geometry : angle 0.65564 ( 7843) SS BOND : bond 0.00782 ( 4) SS BOND : angle 2.28525 ( 8) hydrogen bonds : bond 0.03361 ( 389) hydrogen bonds : angle 4.65198 ( 1143) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7246 (ttm-80) REVERT: A 154 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7806 (mtmm) REVERT: A 198 MET cc_start: 0.7629 (mmt) cc_final: 0.6956 (tpt) REVERT: A 412 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7141 (mtm110) REVERT: A 420 ARG cc_start: 0.6192 (ttt180) cc_final: 0.5377 (ppt90) REVERT: B 40 PHE cc_start: 0.5664 (OUTLIER) cc_final: 0.5069 (t80) outliers start: 23 outliers final: 16 residues processed: 98 average time/residue: 0.4790 time to fit residues: 49.5048 Evaluate side-chains 99 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 40 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 29 optimal weight: 0.0470 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 0.0070 chunk 0 optimal weight: 5.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.193877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.148530 restraints weight = 6454.122| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.96 r_work: 0.3403 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5735 Z= 0.112 Angle : 0.624 10.566 7851 Z= 0.290 Chirality : 0.038 0.277 944 Planarity : 0.005 0.053 996 Dihedral : 4.414 54.260 857 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.92 % Favored : 96.91 % Rotamer: Outliers : 4.19 % Allowed : 30.19 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.37), residues: 582 helix: 1.83 (0.26), residues: 433 sheet: None (None), residues: 0 loop : -0.41 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 352 TYR 0.017 0.001 TYR A 410 PHE 0.014 0.001 PHE A 230 TRP 0.012 0.001 TRP A 291 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5731) covalent geometry : angle 0.62079 ( 7843) SS BOND : bond 0.00577 ( 4) SS BOND : angle 1.94710 ( 8) hydrogen bonds : bond 0.03077 ( 389) hydrogen bonds : angle 4.47527 ( 1143) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.196 Fit side-chains REVERT: A 65 TRP cc_start: 0.4835 (OUTLIER) cc_final: 0.3773 (p-90) REVERT: A 132 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.5583 (ttp80) REVERT: A 139 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7154 (ttm-80) REVERT: A 154 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7579 (mtmm) REVERT: A 198 MET cc_start: 0.7761 (mmt) cc_final: 0.6374 (pmm) REVERT: A 412 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7104 (ttm-80) REVERT: A 420 ARG cc_start: 0.6103 (ttt180) cc_final: 0.5303 (ppt90) REVERT: B 40 PHE cc_start: 0.5457 (OUTLIER) cc_final: 0.5056 (t80) outliers start: 20 outliers final: 11 residues processed: 94 average time/residue: 0.5037 time to fit residues: 49.8622 Evaluate side-chains 94 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 40 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 49 optimal weight: 0.3980 chunk 59 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.193813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148357 restraints weight = 6377.853| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.95 r_work: 0.3571 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 5735 Z= 0.262 Angle : 1.093 59.200 7851 Z= 0.626 Chirality : 0.042 0.562 944 Planarity : 0.005 0.053 996 Dihedral : 4.412 54.178 857 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.09 % Favored : 96.74 % Rotamer: Outliers : 4.19 % Allowed : 30.82 % Favored : 64.99 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.37), residues: 582 helix: 1.83 (0.26), residues: 433 sheet: None (None), residues: 0 loop : -0.45 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 132 TYR 0.020 0.002 TYR A 32 PHE 0.013 0.001 PHE A 534 TRP 0.012 0.001 TRP A 291 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 5731) covalent geometry : angle 1.09136 ( 7843) SS BOND : bond 0.00598 ( 4) SS BOND : angle 1.92892 ( 8) hydrogen bonds : bond 0.03228 ( 389) hydrogen bonds : angle 4.47349 ( 1143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.98 seconds wall clock time: 43 minutes 23.10 seconds (2603.10 seconds total)