Starting phenix.real_space_refine on Thu Jun 5 01:51:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7woc_32648/06_2025/7woc_32648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7woc_32648/06_2025/7woc_32648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7woc_32648/06_2025/7woc_32648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7woc_32648/06_2025/7woc_32648.map" model { file = "/net/cci-nas-00/data/ceres_data/7woc_32648/06_2025/7woc_32648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7woc_32648/06_2025/7woc_32648.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.001 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 18 5.16 5 C 3012 2.51 5 N 804 2.21 5 O 912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4746 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1560 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.29, per 1000 atoms: 0.90 Number of scatterers: 4746 At special positions: 0 Unit cell: (91.02, 68.06, 119.72, 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 18 16.00 O 912 8.00 N 804 7.00 C 3012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " 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 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 599.0 milliseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 14 sheets defined 6.1% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.904A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.612A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.836A pdb=" N ASP A 90 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.749A pdb=" N LYS B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.766A pdb=" N LYS B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 185 through 190' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.543A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.663A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.724A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.568A pdb=" N VAL A 20 " --> pdb=" O MET A 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.604A pdb=" N ILE A 57 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 92 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 116 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.835A pdb=" N LEU A 148 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 145 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 185 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 188 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS A 171 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 157 through 159 removed outlier: 3.722A pdb=" N LYS A 216 " --> pdb=" O CYS A 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 6 removed outlier: 4.340A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.726A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR B 98 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB4, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.742A pdb=" N PHE B 117 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 136 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 134 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASN B 138 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 176 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 147 through 149 88 hydrogen bonds defined for protein. 228 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: 1.29 Time building geometry restraints manager: 1.34 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: 1519 1.34 - 1.46: 1179 1.46 - 1.58: 2147 1.58 - 1.70: 0 1.70 - 1.81: 20 Bond restraints: 4865 Sorted by residual: bond pdb=" C PHE A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.20e-02 6.94e+03 4.78e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C5 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C GLU A 155 " pdb=" N PRO A 156 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.04e+00 bond pdb=" C3 NAG C 601 " pdb=" O3 NAG C 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.02e+00 ... (remaining 4860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 6425 1.10 - 2.21: 131 2.21 - 3.31: 42 3.31 - 4.42: 10 4.42 - 5.52: 9 Bond angle restraints: 6617 Sorted by residual: angle pdb=" C VAL B 151 " pdb=" N ASP B 152 " pdb=" CA ASP B 152 " ideal model delta sigma weight residual 121.54 126.42 -4.88 1.91e+00 2.74e-01 6.52e+00 angle pdb=" C PRO A 154 " pdb=" N GLU A 155 " pdb=" CA GLU A 155 " ideal model delta sigma weight residual 120.26 123.62 -3.36 1.34e+00 5.57e-01 6.28e+00 angle pdb=" N ASP B 152 " pdb=" CA ASP B 152 " pdb=" C ASP B 152 " ideal model delta sigma weight residual 110.80 115.23 -4.43 2.13e+00 2.20e-01 4.32e+00 angle pdb=" N GLY B 69 " pdb=" CA GLY B 69 " pdb=" C GLY B 69 " ideal model delta sigma weight residual 113.18 117.74 -4.56 2.37e+00 1.78e-01 3.70e+00 angle pdb=" CA LYS A 208 " pdb=" C LYS A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 118.44 121.34 -2.90 1.59e+00 3.96e-01 3.33e+00 ... (remaining 6612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 2783 17.48 - 34.96: 101 34.96 - 52.44: 15 52.44 - 69.91: 9 69.91 - 87.39: 3 Dihedral angle restraints: 2911 sinusoidal: 1142 harmonic: 1769 Sorted by residual: dihedral pdb=" CA VAL B 151 " pdb=" C VAL B 151 " pdb=" N ASP B 152 " pdb=" CA ASP B 152 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA CYS C 379 " pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " ideal model delta sinusoidal sigma weight residual 79.00 11.66 67.34 1 2.00e+01 2.50e-03 1.48e+01 dihedral pdb=" SG CYS C 391 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sinusoidal sigma weight residual -73.00 -16.98 -56.02 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 2908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 400 0.025 - 0.050: 198 0.050 - 0.076: 58 0.076 - 0.101: 54 0.101 - 0.126: 19 Chirality restraints: 729 Sorted by residual: chirality pdb=" CA ILE B 59 " pdb=" N ILE B 59 " pdb=" C ILE B 59 " pdb=" CB ILE B 59 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA VAL A 157 " pdb=" N VAL A 157 " pdb=" C VAL A 157 " pdb=" CB VAL A 157 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 726 not shown) Planarity restraints: 856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 521 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 40 " 0.030 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO A 41 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 14 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO B 15 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 15 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 15 " 0.016 5.00e-02 4.00e+02 ... (remaining 853 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1314 2.81 - 3.33: 4052 3.33 - 3.86: 7727 3.86 - 4.38: 8853 4.38 - 4.90: 15570 Nonbonded interactions: 37516 Sorted by model distance: nonbonded pdb=" O GLU B 124 " pdb=" OG SER B 128 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR A 69 " pdb=" OE1 GLU A 82 " model vdw 2.320 3.040 nonbonded pdb=" OD1 ASN A 206 " pdb=" NZ LYS A 213 " model vdw 2.342 3.120 nonbonded pdb=" OD1 ASN C 448 " pdb=" ND2 ASN C 450 " model vdw 2.348 3.120 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.352 3.040 ... (remaining 37511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.950 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4874 Z= 0.101 Angle : 0.478 5.523 6636 Z= 0.256 Chirality : 0.041 0.126 729 Planarity : 0.004 0.047 855 Dihedral : 9.585 87.392 1755 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.60 % Allowed : 6.51 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.27), residues: 600 helix: -4.88 (0.19), residues: 36 sheet: -2.38 (0.36), residues: 175 loop : -3.63 (0.24), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 353 HIS 0.001 0.000 HIS B 33 PHE 0.005 0.001 PHE B 140 TYR 0.005 0.001 TYR B 92 ARG 0.002 0.000 ARG A 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 0.85623 ( 3) hydrogen bonds : bond 0.31233 ( 88) hydrogen bonds : angle 11.57589 ( 228) SS BOND : bond 0.00061 ( 8) SS BOND : angle 0.65785 ( 16) covalent geometry : bond 0.00204 ( 4865) covalent geometry : angle 0.47711 ( 6617) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 455 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7407 (tt) REVERT: A 122 SER cc_start: 0.8289 (m) cc_final: 0.7911 (p) REVERT: B 119 PHE cc_start: 0.5808 (m-80) cc_final: 0.5002 (m-80) REVERT: B 150 LYS cc_start: 0.5451 (mttp) cc_final: 0.5202 (tptp) REVERT: B 174 TYR cc_start: 0.7071 (m-80) cc_final: 0.6470 (m-80) outliers start: 24 outliers final: 7 residues processed: 189 average time/residue: 0.2259 time to fit residues: 51.1674 Evaluate side-chains 108 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.0030 chunk 18 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 439 ASN C 493 GLN A 1 GLN A 178 GLN B 30 ASN B 125 GLN B 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.157332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.126063 restraints weight = 7438.415| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.91 r_work: 0.3494 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4874 Z= 0.129 Angle : 0.623 9.939 6636 Z= 0.310 Chirality : 0.044 0.170 729 Planarity : 0.005 0.046 855 Dihedral : 6.124 83.622 696 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 4.98 % Allowed : 13.98 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.30), residues: 600 helix: -4.75 (0.35), residues: 26 sheet: -2.19 (0.33), residues: 217 loop : -3.00 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 36 HIS 0.005 0.001 HIS A 171 PHE 0.017 0.002 PHE B 47 TYR 0.012 0.002 TYR B 92 ARG 0.006 0.001 ARG B 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 1) link_NAG-ASN : angle 1.13968 ( 3) hydrogen bonds : bond 0.04009 ( 88) hydrogen bonds : angle 7.57867 ( 228) SS BOND : bond 0.00250 ( 8) SS BOND : angle 1.41662 ( 16) covalent geometry : bond 0.00308 ( 4865) covalent geometry : angle 0.62001 ( 6617) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 455 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7815 (tt) REVERT: A 122 SER cc_start: 0.8614 (m) cc_final: 0.8173 (p) REVERT: A 171 HIS cc_start: 0.7312 (m170) cc_final: 0.6704 (m170) REVERT: A 214 VAL cc_start: 0.7307 (OUTLIER) cc_final: 0.7041 (p) REVERT: B 150 LYS cc_start: 0.5304 (mttp) cc_final: 0.4914 (tptp) outliers start: 26 outliers final: 21 residues processed: 119 average time/residue: 0.1966 time to fit residues: 28.8335 Evaluate side-chains 113 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 41 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: C 354 ASN B 148 GLN B 167 GLN 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 = 0.149419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.119023 restraints weight = 7481.230| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.29 r_work: 0.3395 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4874 Z= 0.164 Angle : 0.624 8.396 6636 Z= 0.313 Chirality : 0.045 0.157 729 Planarity : 0.005 0.045 855 Dihedral : 6.348 78.622 696 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 6.13 % Allowed : 15.71 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.31), residues: 600 helix: -4.20 (0.57), residues: 32 sheet: -1.86 (0.35), residues: 213 loop : -2.77 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 149 HIS 0.004 0.001 HIS A 207 PHE 0.021 0.002 PHE B 47 TYR 0.014 0.002 TYR B 92 ARG 0.005 0.001 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 1) link_NAG-ASN : angle 1.31648 ( 3) hydrogen bonds : bond 0.03529 ( 88) hydrogen bonds : angle 6.92604 ( 228) SS BOND : bond 0.00367 ( 8) SS BOND : angle 1.18832 ( 16) covalent geometry : bond 0.00395 ( 4865) covalent geometry : angle 0.62138 ( 6617) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 455 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7991 (tt) REVERT: C 456 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8039 (p90) REVERT: A 13 ARG cc_start: 0.8149 (mmm160) cc_final: 0.7725 (mmp-170) REVERT: A 171 HIS cc_start: 0.7620 (m170) cc_final: 0.7143 (m170) REVERT: B 82 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8038 (pp20) REVERT: B 83 ASP cc_start: 0.8729 (m-30) cc_final: 0.8357 (m-30) REVERT: B 143 ARG cc_start: 0.7230 (tmt-80) cc_final: 0.6979 (tmt-80) REVERT: B 149 TRP cc_start: 0.4689 (m100) cc_final: 0.4180 (m100) REVERT: B 150 LYS cc_start: 0.5695 (mttp) cc_final: 0.5124 (tptp) outliers start: 32 outliers final: 21 residues processed: 109 average time/residue: 0.2508 time to fit residues: 33.8828 Evaluate side-chains 101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 24 optimal weight: 0.3980 chunk 32 optimal weight: 0.0030 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 ASN B 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.151658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120676 restraints weight = 7470.305| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.15 r_work: 0.3426 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4874 Z= 0.103 Angle : 0.555 6.594 6636 Z= 0.277 Chirality : 0.043 0.161 729 Planarity : 0.004 0.042 855 Dihedral : 6.123 78.474 696 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.79 % Allowed : 17.05 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.32), residues: 600 helix: -4.05 (0.66), residues: 32 sheet: -1.44 (0.37), residues: 206 loop : -2.70 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS A 207 PHE 0.011 0.001 PHE B 47 TYR 0.012 0.001 TYR A 105 ARG 0.004 0.000 ARG B 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00018 ( 1) link_NAG-ASN : angle 1.05364 ( 3) hydrogen bonds : bond 0.02954 ( 88) hydrogen bonds : angle 6.61989 ( 228) SS BOND : bond 0.00343 ( 8) SS BOND : angle 0.94516 ( 16) covalent geometry : bond 0.00248 ( 4865) covalent geometry : angle 0.55308 ( 6617) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 455 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7901 (tt) REVERT: A 13 ARG cc_start: 0.8133 (mmm160) cc_final: 0.7726 (mmp-170) REVERT: A 158 THR cc_start: 0.7300 (m) cc_final: 0.6820 (p) REVERT: A 171 HIS cc_start: 0.7649 (m170) cc_final: 0.7067 (m-70) REVERT: B 43 GLN cc_start: 0.8164 (pt0) cc_final: 0.7914 (pt0) REVERT: B 82 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7989 (pp20) REVERT: B 83 ASP cc_start: 0.8682 (m-30) cc_final: 0.8097 (m-30) REVERT: B 149 TRP cc_start: 0.4629 (m100) cc_final: 0.4374 (m100) REVERT: B 150 LYS cc_start: 0.5559 (mttp) cc_final: 0.5247 (tptp) outliers start: 25 outliers final: 18 residues processed: 105 average time/residue: 0.1959 time to fit residues: 25.4457 Evaluate side-chains 104 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.146065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.115301 restraints weight = 7639.057| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.19 r_work: 0.3344 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4874 Z= 0.178 Angle : 0.624 7.477 6636 Z= 0.314 Chirality : 0.046 0.150 729 Planarity : 0.005 0.039 855 Dihedral : 6.292 72.314 695 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 5.75 % Allowed : 16.09 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.32), residues: 600 helix: -3.83 (0.59), residues: 38 sheet: -1.51 (0.35), residues: 215 loop : -2.66 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 149 HIS 0.005 0.001 HIS A 207 PHE 0.019 0.002 PHE B 47 TYR 0.014 0.002 TYR B 92 ARG 0.004 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 1) link_NAG-ASN : angle 1.22547 ( 3) hydrogen bonds : bond 0.03223 ( 88) hydrogen bonds : angle 6.64716 ( 228) SS BOND : bond 0.00269 ( 8) SS BOND : angle 1.12503 ( 16) covalent geometry : bond 0.00427 ( 4865) covalent geometry : angle 0.62147 ( 6617) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8635 (tmm160) cc_final: 0.8434 (ttp80) REVERT: C 455 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8061 (tt) REVERT: C 456 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.7994 (p90) REVERT: A 13 ARG cc_start: 0.8164 (mmm160) cc_final: 0.7759 (mmp-170) REVERT: A 158 THR cc_start: 0.7385 (m) cc_final: 0.6870 (p) REVERT: A 171 HIS cc_start: 0.7788 (m170) cc_final: 0.7394 (m-70) REVERT: B 82 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7875 (pp20) REVERT: B 83 ASP cc_start: 0.8634 (m-30) cc_final: 0.7869 (m-30) REVERT: B 119 PHE cc_start: 0.6219 (m-10) cc_final: 0.5939 (m-80) REVERT: B 149 TRP cc_start: 0.4760 (m100) cc_final: 0.4506 (m100) REVERT: B 150 LYS cc_start: 0.5890 (mttp) cc_final: 0.5198 (tptp) outliers start: 30 outliers final: 26 residues processed: 109 average time/residue: 0.2070 time to fit residues: 28.3492 Evaluate side-chains 110 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.146210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115081 restraints weight = 7661.122| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.17 r_work: 0.3349 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4874 Z= 0.154 Angle : 0.600 6.988 6636 Z= 0.303 Chirality : 0.046 0.180 729 Planarity : 0.004 0.037 855 Dihedral : 6.275 70.992 695 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 5.56 % Allowed : 17.24 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.33), residues: 600 helix: -3.92 (0.54), residues: 38 sheet: -1.35 (0.36), residues: 211 loop : -2.57 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 149 HIS 0.005 0.001 HIS A 207 PHE 0.018 0.002 PHE B 47 TYR 0.014 0.002 TYR A 32 ARG 0.004 0.001 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 1) link_NAG-ASN : angle 1.14152 ( 3) hydrogen bonds : bond 0.02980 ( 88) hydrogen bonds : angle 6.44862 ( 228) SS BOND : bond 0.00347 ( 8) SS BOND : angle 1.01768 ( 16) covalent geometry : bond 0.00373 ( 4865) covalent geometry : angle 0.59827 ( 6617) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8650 (tmm160) cc_final: 0.8448 (ttp80) REVERT: C 455 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7991 (tt) REVERT: C 456 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8035 (p90) REVERT: A 158 THR cc_start: 0.7423 (m) cc_final: 0.6908 (p) REVERT: A 171 HIS cc_start: 0.7901 (m170) cc_final: 0.7489 (m-70) REVERT: B 83 ASP cc_start: 0.8715 (m-30) cc_final: 0.8438 (m-30) REVERT: B 119 PHE cc_start: 0.6238 (m-10) cc_final: 0.6020 (m-80) REVERT: B 150 LYS cc_start: 0.6086 (mttp) cc_final: 0.5412 (tptp) outliers start: 29 outliers final: 21 residues processed: 97 average time/residue: 0.1915 time to fit residues: 23.2129 Evaluate side-chains 100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.144978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.113681 restraints weight = 7556.689| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.01 r_work: 0.3343 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4874 Z= 0.161 Angle : 0.618 8.203 6636 Z= 0.312 Chirality : 0.046 0.163 729 Planarity : 0.004 0.038 855 Dihedral : 6.316 70.844 694 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 5.36 % Allowed : 17.82 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.33), residues: 600 helix: -3.96 (0.52), residues: 38 sheet: -1.35 (0.38), residues: 198 loop : -2.51 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.006 0.001 HIS A 207 PHE 0.017 0.002 PHE B 47 TYR 0.014 0.002 TYR A 105 ARG 0.004 0.001 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 1) link_NAG-ASN : angle 1.12841 ( 3) hydrogen bonds : bond 0.02979 ( 88) hydrogen bonds : angle 6.31195 ( 228) SS BOND : bond 0.00313 ( 8) SS BOND : angle 1.06750 ( 16) covalent geometry : bond 0.00388 ( 4865) covalent geometry : angle 0.61611 ( 6617) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8643 (tmm160) cc_final: 0.8366 (ttp80) REVERT: C 455 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8007 (tt) REVERT: C 456 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8020 (p90) REVERT: A 13 ARG cc_start: 0.8110 (mmm160) cc_final: 0.7730 (mmp-170) REVERT: A 158 THR cc_start: 0.7479 (m) cc_final: 0.6956 (p) REVERT: B 83 ASP cc_start: 0.8762 (m-30) cc_final: 0.8506 (m-30) REVERT: B 119 PHE cc_start: 0.6265 (m-10) cc_final: 0.6062 (m-80) REVERT: B 150 LYS cc_start: 0.6185 (mttp) cc_final: 0.5476 (tptp) outliers start: 28 outliers final: 25 residues processed: 97 average time/residue: 0.2932 time to fit residues: 36.1251 Evaluate side-chains 104 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.145613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.113823 restraints weight = 7554.155| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.96 r_work: 0.3353 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4874 Z= 0.141 Angle : 0.611 7.861 6636 Z= 0.309 Chirality : 0.046 0.151 729 Planarity : 0.004 0.039 855 Dihedral : 6.152 70.211 693 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.79 % Allowed : 19.92 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.33), residues: 600 helix: -3.84 (0.54), residues: 38 sheet: -1.54 (0.37), residues: 206 loop : -2.34 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 PHE 0.016 0.001 PHE B 47 TYR 0.014 0.002 TYR A 105 ARG 0.005 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 1) link_NAG-ASN : angle 1.10665 ( 3) hydrogen bonds : bond 0.02910 ( 88) hydrogen bonds : angle 6.21197 ( 228) SS BOND : bond 0.00279 ( 8) SS BOND : angle 0.77716 ( 16) covalent geometry : bond 0.00342 ( 4865) covalent geometry : angle 0.60976 ( 6617) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8628 (tmm160) cc_final: 0.8351 (ttp80) REVERT: C 455 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8015 (tt) REVERT: C 456 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8005 (p90) REVERT: A 158 THR cc_start: 0.7441 (m) cc_final: 0.6902 (p) REVERT: A 171 HIS cc_start: 0.7819 (m90) cc_final: 0.7391 (m-70) REVERT: B 83 ASP cc_start: 0.8717 (m-30) cc_final: 0.8487 (m-30) REVERT: B 150 LYS cc_start: 0.6123 (mttp) cc_final: 0.5557 (tptp) outliers start: 25 outliers final: 20 residues processed: 100 average time/residue: 0.1989 time to fit residues: 24.8362 Evaluate side-chains 103 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 0.0470 chunk 55 optimal weight: 4.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.143817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.111752 restraints weight = 7566.524| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.94 r_work: 0.3324 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 4874 Z= 0.186 Angle : 0.653 8.570 6636 Z= 0.332 Chirality : 0.046 0.158 729 Planarity : 0.005 0.041 855 Dihedral : 6.354 69.639 693 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 4.98 % Allowed : 20.11 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.33), residues: 600 helix: -3.74 (0.53), residues: 44 sheet: -1.40 (0.37), residues: 203 loop : -2.48 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.006 0.001 HIS A 207 PHE 0.020 0.002 PHE B 47 TYR 0.016 0.002 TYR A 105 ARG 0.004 0.001 ARG B 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 1) link_NAG-ASN : angle 1.15429 ( 3) hydrogen bonds : bond 0.03201 ( 88) hydrogen bonds : angle 6.27526 ( 228) SS BOND : bond 0.00320 ( 8) SS BOND : angle 0.95130 ( 16) covalent geometry : bond 0.00450 ( 4865) covalent geometry : angle 0.65213 ( 6617) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8653 (tmm160) cc_final: 0.8358 (ttp80) REVERT: C 455 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8015 (tt) REVERT: C 456 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8066 (p90) REVERT: A 13 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7735 (mmp-170) REVERT: B 83 ASP cc_start: 0.8748 (m-30) cc_final: 0.8509 (m-30) REVERT: B 150 LYS cc_start: 0.6687 (mttp) cc_final: 0.5885 (tptp) outliers start: 26 outliers final: 23 residues processed: 94 average time/residue: 0.2097 time to fit residues: 24.4945 Evaluate side-chains 102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.145276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.113204 restraints weight = 7573.409| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.99 r_work: 0.3345 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4874 Z= 0.141 Angle : 0.629 9.334 6636 Z= 0.317 Chirality : 0.046 0.143 729 Planarity : 0.004 0.042 855 Dihedral : 6.070 66.811 693 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 4.60 % Allowed : 20.69 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.33), residues: 600 helix: -3.85 (0.56), residues: 38 sheet: -1.53 (0.37), residues: 208 loop : -2.21 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 PHE 0.015 0.001 PHE B 47 TYR 0.016 0.002 TYR A 105 ARG 0.004 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 1) link_NAG-ASN : angle 1.21405 ( 3) hydrogen bonds : bond 0.03157 ( 88) hydrogen bonds : angle 6.14930 ( 228) SS BOND : bond 0.00300 ( 8) SS BOND : angle 0.80559 ( 16) covalent geometry : bond 0.00343 ( 4865) covalent geometry : angle 0.62775 ( 6617) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8657 (tmm160) cc_final: 0.8367 (ttp80) REVERT: C 455 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7984 (tt) REVERT: C 456 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7989 (p90) REVERT: A 13 ARG cc_start: 0.8110 (mmm160) cc_final: 0.7740 (mmp-170) REVERT: A 158 THR cc_start: 0.7557 (m) cc_final: 0.7001 (p) REVERT: B 83 ASP cc_start: 0.8710 (m-30) cc_final: 0.8466 (m-30) REVERT: B 150 LYS cc_start: 0.6762 (mttp) cc_final: 0.6073 (tptp) outliers start: 24 outliers final: 22 residues processed: 96 average time/residue: 0.1961 time to fit residues: 23.5789 Evaluate side-chains 104 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 48 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.144064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113481 restraints weight = 7606.273| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.00 r_work: 0.3341 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4874 Z= 0.153 Angle : 0.641 8.526 6636 Z= 0.323 Chirality : 0.046 0.145 729 Planarity : 0.004 0.042 855 Dihedral : 5.960 66.227 693 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 4.79 % Allowed : 20.69 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.34), residues: 600 helix: -3.87 (0.57), residues: 38 sheet: -1.50 (0.37), residues: 208 loop : -2.18 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 PHE 0.016 0.002 PHE B 47 TYR 0.016 0.002 TYR A 105 ARG 0.004 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 1) link_NAG-ASN : angle 1.17931 ( 3) hydrogen bonds : bond 0.03235 ( 88) hydrogen bonds : angle 6.15391 ( 228) SS BOND : bond 0.00299 ( 8) SS BOND : angle 0.82644 ( 16) covalent geometry : bond 0.00372 ( 4865) covalent geometry : angle 0.63994 ( 6617) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3907.77 seconds wall clock time: 70 minutes 2.65 seconds (4202.65 seconds total)