Starting phenix.real_space_refine on Tue Feb 3 16:52:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kl0_62398/02_2026/9kl0_62398.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kl0_62398/02_2026/9kl0_62398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kl0_62398/02_2026/9kl0_62398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kl0_62398/02_2026/9kl0_62398.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kl0_62398/02_2026/9kl0_62398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kl0_62398/02_2026/9kl0_62398.map" } resolution = 3.16 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= 0.110 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 33 5.16 5 C 3335 2.51 5 N 869 2.21 5 O 899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 5136 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3811 Classifications: {'peptide': 503} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 478} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 229 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 28} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 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: 1.48, per 1000 atoms: 0.29 Number of scatterers: 5136 At special positions: 0 Unit cell: (89.628, 71.489, 114.169, 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 33 16.00 O 899 8.00 N 869 7.00 C 3335 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=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.04 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: 0.50 Conformation dependent library (CDL) restraints added in 315.2 milliseconds 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1374 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 85.0% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 22 through 44 removed outlier: 3.704A pdb=" N ILE A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.986A pdb=" N ALA A 85 " --> pdb=" O PHE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 removed outlier: 4.231A pdb=" N GLU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 136 through 154 Processing helix chain 'A' and resid 155 through 171 removed outlier: 4.164A pdb=" N GLN A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 191 removed outlier: 3.818A pdb=" N ALA A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.669A pdb=" N ALA A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 207 through 222 removed outlier: 3.751A pdb=" N GLU A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.687A pdb=" N PHE A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) 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 275 through 287 Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.711A pdb=" N THR A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 328 through 339 removed outlier: 3.841A pdb=" N ARG A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 337 " --> pdb=" O MET A 333 " (cutoff:3.500A) 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 374 Processing helix chain 'A' and resid 377 through 409 removed outlier: 3.758A 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 420 through 446 removed outlier: 3.753A pdb=" N GLY A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Proline residue: A 442 - end of helix removed outlier: 3.507A pdb=" N ALA A 446 " --> pdb=" O PRO A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 477 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 481 through 501 removed outlier: 3.992A pdb=" N ARG A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 525 through 549 removed outlier: 3.965A pdb=" N ALA A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 671 Processing helix chain 'B' and resid 28 through 54 removed outlier: 3.840A pdb=" N ASN B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.537A pdb=" N UNK H 91 " --> pdb=" O UNK H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 104 removed outlier: 3.896A 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 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.603A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N UNK H 33 " --> pdb=" O UNK H 99 " (cutoff:3.500A) removed outlier: 4.089A 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: 6.603A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 5.650A 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 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.269A pdb=" N UNK L 11 " --> pdb=" O UNK L 105 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1065 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: 0.91 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1665 1.34 - 1.46: 1232 1.46 - 1.58: 2288 1.58 - 1.70: 0 1.70 - 1.82: 52 Bond restraints: 5237 Sorted by residual: bond pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " ideal model delta sigma weight residual 1.808 1.747 0.061 3.30e-02 9.18e+02 3.45e+00 bond pdb=" N UNK L 1 " pdb=" CA UNK L 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.55e+00 bond pdb=" N UNK H 1 " pdb=" CA UNK H 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.53e+00 bond pdb=" CG PRO A 478 " pdb=" CD PRO A 478 " ideal model delta sigma weight residual 1.503 1.458 0.045 3.40e-02 8.65e+02 1.75e+00 bond pdb=" C UNK L 94 " pdb=" N UNK L 95 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.40e-02 5.10e+03 1.01e+00 ... (remaining 5232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 6644 1.36 - 2.73: 426 2.73 - 4.09: 81 4.09 - 5.46: 14 5.46 - 6.82: 6 Bond angle restraints: 7171 Sorted by residual: angle pdb=" N VAL A 105 " pdb=" CA VAL A 105 " pdb=" C VAL A 105 " ideal model delta sigma weight residual 111.45 108.16 3.29 9.30e-01 1.16e+00 1.25e+01 angle pdb=" N CYS A 361 " pdb=" CA CYS A 361 " pdb=" C CYS A 361 " ideal model delta sigma weight residual 110.06 114.69 -4.63 1.43e+00 4.89e-01 1.05e+01 angle pdb=" CA CYS A 361 " pdb=" CB CYS A 361 " pdb=" SG CYS A 361 " ideal model delta sigma weight residual 114.40 107.58 6.82 2.30e+00 1.89e-01 8.80e+00 angle pdb=" N CYS A 355 " pdb=" CA CYS A 355 " pdb=" CB CYS A 355 " ideal model delta sigma weight residual 110.63 104.90 5.73 1.94e+00 2.66e-01 8.71e+00 angle pdb=" CA CYS A 355 " pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " ideal model delta sigma weight residual 114.40 120.83 -6.43 2.30e+00 1.89e-01 7.82e+00 ... (remaining 7166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 2651 15.99 - 31.98: 275 31.98 - 47.98: 70 47.98 - 63.97: 12 63.97 - 79.96: 4 Dihedral angle restraints: 3012 sinusoidal: 868 harmonic: 2144 Sorted by residual: dihedral pdb=" CA CYS A 255 " pdb=" C CYS A 255 " pdb=" N TYR A 256 " pdb=" CA TYR A 256 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA VAL A 354 " pdb=" C VAL A 354 " pdb=" N CYS A 355 " pdb=" CA CYS A 355 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA GLU A 503 " pdb=" C GLU A 503 " pdb=" N PHE A 504 " pdb=" CA PHE A 504 " ideal model delta harmonic sigma weight residual 180.00 162.40 17.60 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 3009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 597 0.035 - 0.070: 197 0.070 - 0.105: 67 0.105 - 0.140: 12 0.140 - 0.175: 3 Chirality restraints: 876 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 2.47 0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CA CYS A 361 " pdb=" N CYS A 361 " pdb=" C CYS A 361 " pdb=" CB CYS A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CB VAL A 665 " pdb=" CA VAL A 665 " pdb=" CG1 VAL A 665 " pdb=" CG2 VAL A 665 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 873 not shown) Planarity restraints: 911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 477 " 0.058 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO A 478 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 478 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 478 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 464 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 465 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 465 " -0.029 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=" C ILE A 501 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 502 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.027 5.00e-02 4.00e+02 ... (remaining 908 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1984 2.86 - 3.37: 5108 3.37 - 3.88: 8188 3.88 - 4.39: 9295 4.39 - 4.90: 15542 Nonbonded interactions: 40117 Sorted by model distance: nonbonded pdb=" OD1 ASP A 25 " pdb=" N GLY A 380 " model vdw 2.355 3.120 nonbonded pdb=" O PHE B 48 " pdb=" OD1 ASN B 51 " model vdw 2.364 3.040 nonbonded pdb=" O LEU A 140 " pdb=" OG SER A 143 " model vdw 2.373 3.040 nonbonded pdb=" O ILE A 433 " pdb=" OG SER A 437 " model vdw 2.393 3.040 nonbonded pdb=" N UNK H 100 " pdb=" O UNK H 105 " model vdw 2.393 3.120 ... (remaining 40112 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.730 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 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 0.061 5241 Z= 0.187 Angle : 0.787 8.471 7179 Z= 0.385 Chirality : 0.040 0.175 876 Planarity : 0.006 0.088 911 Dihedral : 14.596 79.959 1626 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 30.02 % Favored : 69.98 % 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: 0.55 (0.39), residues: 521 helix: 0.99 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -1.21 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 139 TYR 0.014 0.001 TYR A 256 PHE 0.017 0.001 PHE A 504 TRP 0.018 0.001 TRP B 30 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 5237) covalent geometry : angle 0.78065 ( 7171) SS BOND : bond 0.00492 ( 4) SS BOND : angle 3.09801 ( 8) hydrogen bonds : bond 0.14856 ( 353) hydrogen bonds : angle 7.87323 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.178 Fit side-chains REVERT: A 109 LEU cc_start: 0.7698 (mt) cc_final: 0.7456 (mt) REVERT: A 268 HIS cc_start: 0.8059 (t-90) cc_final: 0.7718 (t-90) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0711 time to fit residues: 8.2538 Evaluate side-chains 87 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.181079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.147103 restraints weight = 6690.075| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.99 r_work: 0.3640 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5241 Z= 0.166 Angle : 0.663 7.914 7179 Z= 0.314 Chirality : 0.040 0.170 876 Planarity : 0.005 0.065 911 Dihedral : 3.943 21.171 791 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.96 % Allowed : 24.82 % Favored : 70.21 % 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: 0.95 (0.39), residues: 521 helix: 1.11 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -0.70 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.014 0.002 TYR A 256 PHE 0.017 0.002 PHE A 486 TRP 0.018 0.001 TRP A 276 HIS 0.002 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 5237) covalent geometry : angle 0.65790 ( 7171) SS BOND : bond 0.00510 ( 4) SS BOND : angle 2.49247 ( 8) hydrogen bonds : bond 0.03634 ( 353) hydrogen bonds : angle 5.52807 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.134 Fit side-chains REVERT: A 145 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8320 (mp) REVERT: A 187 ILE cc_start: 0.8381 (mm) cc_final: 0.8070 (mp) REVERT: A 204 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7498 (mm110) REVERT: A 268 HIS cc_start: 0.8226 (t-90) cc_final: 0.7749 (t-90) outliers start: 21 outliers final: 11 residues processed: 104 average time/residue: 0.0692 time to fit residues: 9.3552 Evaluate side-chains 104 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 542 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 0 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.182413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148489 restraints weight = 6589.757| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.98 r_work: 0.3655 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5241 Z= 0.141 Angle : 0.618 10.154 7179 Z= 0.291 Chirality : 0.038 0.165 876 Planarity : 0.005 0.064 911 Dihedral : 3.832 23.399 791 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.96 % Allowed : 26.00 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.40), residues: 521 helix: 1.27 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -0.55 (0.66), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.013 0.001 TYR A 256 PHE 0.011 0.001 PHE A 230 TRP 0.019 0.001 TRP A 276 HIS 0.001 0.000 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5237) covalent geometry : angle 0.61295 ( 7171) SS BOND : bond 0.00190 ( 4) SS BOND : angle 2.54712 ( 8) hydrogen bonds : bond 0.03472 ( 353) hydrogen bonds : angle 5.23902 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.197 Fit side-chains REVERT: A 268 HIS cc_start: 0.8284 (t-90) cc_final: 0.7732 (t-90) REVERT: A 414 ARG cc_start: 0.7630 (tpt-90) cc_final: 0.7346 (ttp80) outliers start: 21 outliers final: 14 residues processed: 103 average time/residue: 0.0651 time to fit residues: 9.1613 Evaluate side-chains 100 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 540 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.181582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147064 restraints weight = 6641.213| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.01 r_work: 0.3646 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5241 Z= 0.152 Angle : 0.635 11.321 7179 Z= 0.296 Chirality : 0.039 0.175 876 Planarity : 0.005 0.064 911 Dihedral : 3.812 23.409 791 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.44 % Allowed : 26.95 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.40), residues: 521 helix: 1.27 (0.27), residues: 394 sheet: None (None), residues: 0 loop : -0.55 (0.66), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.014 0.002 TYR A 256 PHE 0.013 0.001 PHE A 230 TRP 0.021 0.001 TRP A 276 HIS 0.001 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5237) covalent geometry : angle 0.62914 ( 7171) SS BOND : bond 0.00654 ( 4) SS BOND : angle 2.67946 ( 8) hydrogen bonds : bond 0.03447 ( 353) hydrogen bonds : angle 5.17663 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8384 (mp) REVERT: A 268 HIS cc_start: 0.8298 (t-90) cc_final: 0.7790 (t-90) REVERT: A 378 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6794 (tp) outliers start: 23 outliers final: 16 residues processed: 97 average time/residue: 0.0653 time to fit residues: 8.5893 Evaluate side-chains 101 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 540 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.181327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144862 restraints weight = 6666.282| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.10 r_work: 0.3603 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 5241 Z= 0.171 Angle : 0.653 11.864 7179 Z= 0.305 Chirality : 0.039 0.182 876 Planarity : 0.005 0.066 911 Dihedral : 3.886 24.407 791 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.86 % Allowed : 25.53 % Favored : 67.61 % 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: 1.13 (0.39), residues: 521 helix: 1.25 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.66 (0.65), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.015 0.002 TYR A 256 PHE 0.014 0.001 PHE A 230 TRP 0.023 0.001 TRP A 276 HIS 0.001 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 5237) covalent geometry : angle 0.64697 ( 7171) SS BOND : bond 0.00641 ( 4) SS BOND : angle 2.78636 ( 8) hydrogen bonds : bond 0.03551 ( 353) hydrogen bonds : angle 5.21437 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.099 Fit side-chains REVERT: A 145 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8323 (mp) REVERT: A 268 HIS cc_start: 0.8288 (t-90) cc_final: 0.7688 (t-90) REVERT: A 378 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.6681 (tp) REVERT: A 668 TRP cc_start: 0.7678 (OUTLIER) cc_final: 0.7139 (t60) outliers start: 29 outliers final: 20 residues processed: 105 average time/residue: 0.0518 time to fit residues: 7.4231 Evaluate side-chains 111 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 668 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 70 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 21 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.183081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146808 restraints weight = 6627.684| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.12 r_work: 0.3623 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5241 Z= 0.141 Angle : 0.636 12.955 7179 Z= 0.292 Chirality : 0.038 0.179 876 Planarity : 0.005 0.065 911 Dihedral : 3.713 23.228 791 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.67 % Allowed : 26.71 % Favored : 67.61 % 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: 1.21 (0.39), residues: 521 helix: 1.28 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -0.53 (0.66), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.013 0.001 TYR A 256 PHE 0.014 0.001 PHE A 486 TRP 0.026 0.001 TRP A 276 HIS 0.001 0.000 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5237) covalent geometry : angle 0.63079 ( 7171) SS BOND : bond 0.00518 ( 4) SS BOND : angle 2.41412 ( 8) hydrogen bonds : bond 0.03374 ( 353) hydrogen bonds : angle 5.09704 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.100 Fit side-chains REVERT: A 145 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8342 (mp) REVERT: A 268 HIS cc_start: 0.8257 (t-90) cc_final: 0.7691 (t-90) REVERT: A 378 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6719 (tp) REVERT: A 421 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6464 (tt0) REVERT: A 668 TRP cc_start: 0.7671 (OUTLIER) cc_final: 0.7150 (t60) outliers start: 24 outliers final: 17 residues processed: 103 average time/residue: 0.0631 time to fit residues: 8.7091 Evaluate side-chains 107 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 668 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 38 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.183391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147283 restraints weight = 6546.067| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.10 r_work: 0.3635 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5241 Z= 0.142 Angle : 0.641 13.494 7179 Z= 0.292 Chirality : 0.038 0.193 876 Planarity : 0.005 0.065 911 Dihedral : 3.691 23.608 791 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.67 % Allowed : 25.77 % Favored : 68.56 % 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: 1.15 (0.39), residues: 521 helix: 1.29 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -0.74 (0.66), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.013 0.001 TYR A 256 PHE 0.012 0.001 PHE A 230 TRP 0.026 0.001 TRP A 276 HIS 0.001 0.000 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5237) covalent geometry : angle 0.63643 ( 7171) SS BOND : bond 0.00497 ( 4) SS BOND : angle 2.34002 ( 8) hydrogen bonds : bond 0.03363 ( 353) hydrogen bonds : angle 5.03228 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.134 Fit side-chains REVERT: A 145 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8416 (mp) REVERT: A 268 HIS cc_start: 0.8268 (t-90) cc_final: 0.7677 (t-90) REVERT: A 378 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6727 (tp) REVERT: A 414 ARG cc_start: 0.7090 (ttt-90) cc_final: 0.6829 (ttp80) REVERT: A 421 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6550 (tt0) REVERT: A 542 LEU cc_start: 0.8027 (mm) cc_final: 0.7624 (mt) REVERT: A 668 TRP cc_start: 0.7695 (OUTLIER) cc_final: 0.7166 (t60) outliers start: 24 outliers final: 18 residues processed: 100 average time/residue: 0.0599 time to fit residues: 8.1484 Evaluate side-chains 103 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 668 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 14 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.177951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141171 restraints weight = 6672.927| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.08 r_work: 0.3563 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 5241 Z= 0.260 Angle : 0.760 11.580 7179 Z= 0.356 Chirality : 0.043 0.214 876 Planarity : 0.005 0.073 911 Dihedral : 4.206 24.899 791 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 6.86 % Allowed : 24.59 % Favored : 68.56 % 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: 0.69 (0.39), residues: 521 helix: 0.95 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -0.87 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 414 TYR 0.018 0.002 TYR A 256 PHE 0.016 0.002 PHE A 670 TRP 0.026 0.002 TRP A 276 HIS 0.002 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00615 ( 5237) covalent geometry : angle 0.75140 ( 7171) SS BOND : bond 0.00800 ( 4) SS BOND : angle 3.58797 ( 8) hydrogen bonds : bond 0.03926 ( 353) hydrogen bonds : angle 5.41736 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8355 (mp) REVERT: A 268 HIS cc_start: 0.8272 (t-90) cc_final: 0.7712 (t-90) REVERT: A 414 ARG cc_start: 0.7201 (ttt-90) cc_final: 0.6761 (ttp80) REVERT: A 421 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6370 (tt0) REVERT: A 668 TRP cc_start: 0.7797 (OUTLIER) cc_final: 0.7220 (t60) outliers start: 29 outliers final: 25 residues processed: 109 average time/residue: 0.0585 time to fit residues: 8.7066 Evaluate side-chains 111 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 668 TRP Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.0870 chunk 32 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.183471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.147381 restraints weight = 6581.390| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.09 r_work: 0.3642 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5241 Z= 0.129 Angle : 0.643 15.114 7179 Z= 0.293 Chirality : 0.038 0.195 876 Planarity : 0.005 0.069 911 Dihedral : 3.722 23.321 791 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 6.15 % Allowed : 25.77 % Favored : 68.09 % 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: 0.95 (0.39), residues: 521 helix: 1.16 (0.27), residues: 394 sheet: None (None), residues: 0 loop : -0.92 (0.65), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.012 0.001 TYR A 128 PHE 0.011 0.001 PHE A 230 TRP 0.027 0.001 TRP A 276 HIS 0.001 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5237) covalent geometry : angle 0.63932 ( 7171) SS BOND : bond 0.00451 ( 4) SS BOND : angle 2.20820 ( 8) hydrogen bonds : bond 0.03357 ( 353) hydrogen bonds : angle 5.02680 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8293 (mp) REVERT: A 268 HIS cc_start: 0.8273 (t-90) cc_final: 0.7678 (t-90) REVERT: A 378 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7129 (tp) REVERT: A 414 ARG cc_start: 0.7070 (ttt-90) cc_final: 0.6661 (ttp80) REVERT: A 542 LEU cc_start: 0.8373 (mm) cc_final: 0.7952 (mt) REVERT: A 668 TRP cc_start: 0.7666 (OUTLIER) cc_final: 0.7139 (t60) outliers start: 26 outliers final: 20 residues processed: 103 average time/residue: 0.0618 time to fit residues: 8.6122 Evaluate side-chains 109 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 668 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.181964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145908 restraints weight = 6607.871| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.08 r_work: 0.3625 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5241 Z= 0.151 Angle : 0.659 14.486 7179 Z= 0.301 Chirality : 0.039 0.235 876 Planarity : 0.005 0.070 911 Dihedral : 3.768 24.098 791 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.20 % Allowed : 26.48 % Favored : 68.32 % 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: 0.99 (0.39), residues: 521 helix: 1.20 (0.27), residues: 394 sheet: None (None), residues: 0 loop : -0.93 (0.65), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.013 0.001 TYR A 256 PHE 0.015 0.001 PHE A 486 TRP 0.033 0.001 TRP A 276 HIS 0.001 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5237) covalent geometry : angle 0.65385 ( 7171) SS BOND : bond 0.00527 ( 4) SS BOND : angle 2.43604 ( 8) hydrogen bonds : bond 0.03462 ( 353) hydrogen bonds : angle 5.03304 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1042 Ramachandran restraints generated. 521 Oldfield, 0 Emsley, 521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8394 (mp) REVERT: A 268 HIS cc_start: 0.8277 (t-90) cc_final: 0.7676 (t-90) REVERT: A 378 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7130 (tp) REVERT: A 421 GLU cc_start: 0.5053 (tt0) cc_final: 0.4766 (tt0) REVERT: A 425 VAL cc_start: 0.7948 (m) cc_final: 0.7699 (t) REVERT: A 542 LEU cc_start: 0.8431 (mm) cc_final: 0.8050 (mt) REVERT: A 661 MET cc_start: 0.7780 (tpp) cc_final: 0.7575 (ttt) REVERT: A 668 TRP cc_start: 0.7714 (OUTLIER) cc_final: 0.7162 (t60) outliers start: 22 outliers final: 19 residues processed: 97 average time/residue: 0.0695 time to fit residues: 9.0807 Evaluate side-chains 105 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 HIS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 668 TRP Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.182009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145939 restraints weight = 6704.408| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.08 r_work: 0.3628 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5241 Z= 0.151 Angle : 0.656 14.349 7179 Z= 0.300 Chirality : 0.039 0.210 876 Planarity : 0.005 0.069 911 Dihedral : 3.769 23.527 791 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.67 % Allowed : 26.48 % Favored : 67.85 % 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: 0.95 (0.39), residues: 521 helix: 1.17 (0.27), residues: 395 sheet: None (None), residues: 0 loop : -0.97 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.014 0.001 TYR A 256 PHE 0.013 0.001 PHE A 230 TRP 0.033 0.001 TRP A 276 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5237) covalent geometry : angle 0.65076 ( 7171) SS BOND : bond 0.00538 ( 4) SS BOND : angle 2.48379 ( 8) hydrogen bonds : bond 0.03441 ( 353) hydrogen bonds : angle 5.01544 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1503.07 seconds wall clock time: 26 minutes 18.46 seconds (1578.46 seconds total)