Starting phenix.real_space_refine on Fri Aug 22 15:27:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ez3_28728/08_2025/8ez3_28728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ez3_28728/08_2025/8ez3_28728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ez3_28728/08_2025/8ez3_28728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ez3_28728/08_2025/8ez3_28728.map" model { file = "/net/cci-nas-00/data/ceres_data/8ez3_28728/08_2025/8ez3_28728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ez3_28728/08_2025/8ez3_28728.cif" } resolution = 2.5 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 ------------------------------------------------------------------------------- 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= 0.123 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 26 5.16 5 C 3039 2.51 5 N 839 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4894 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 815 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2996 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 371} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.34, per 1000 atoms: 0.27 Number of scatterers: 4894 At special positions: 0 Unit cell: (96.46, 80.56, 93.28, 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 26 16.00 O 990 8.00 N 839 7.00 C 3039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " 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 ALPHA1-2 " MAN B 4 " - " MAN B 5 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 329 " " NAG A 504 " - " ASN A 234 " " NAG B 1 " - " ASN A 200 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 193.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 13 sheets defined 3.5% alpha, 43.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'L' and resid 27B through 30 Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.651A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.642A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.054A pdb=" N HIS H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.396A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.511A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.820A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.167A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.858A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.624A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.249A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 311 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.514A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER A 372 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 441 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: 0.77 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1596 1.35 - 1.48: 1352 1.48 - 1.60: 2030 1.60 - 1.73: 0 1.73 - 1.85: 30 Bond restraints: 5008 Sorted by residual: bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.449 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C2 BMA B 3 " pdb=" C3 BMA B 3 " ideal model delta sigma weight residual 1.544 1.513 0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C5 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 5003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 6738 2.57 - 5.15: 62 5.15 - 7.72: 9 7.72 - 10.29: 0 10.29 - 12.86: 1 Bond angle restraints: 6810 Sorted by residual: angle pdb=" CA CYS A 417 " pdb=" CB CYS A 417 " pdb=" SG CYS A 417 " ideal model delta sigma weight residual 114.40 127.26 -12.86 2.30e+00 1.89e-01 3.13e+01 angle pdb=" C GLY L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C HIS A 336 " pdb=" N CYS A 337 " pdb=" CA CYS A 337 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C CYS A 417 " pdb=" CA CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sigma weight residual 109.68 115.29 -5.61 1.98e+00 2.55e-01 8.04e+00 angle pdb=" C ARG A 430 " pdb=" N LYS A 431 " pdb=" CA LYS A 431 " ideal model delta sigma weight residual 121.70 126.41 -4.71 1.80e+00 3.09e-01 6.86e+00 ... (remaining 6805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 2777 23.03 - 46.05: 228 46.05 - 69.08: 49 69.08 - 92.11: 14 92.11 - 115.13: 7 Dihedral angle restraints: 3075 sinusoidal: 1309 harmonic: 1766 Sorted by residual: dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 135.77 -42.77 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 50.93 42.07 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA ASN L 51 " pdb=" C ASN L 51 " pdb=" N SER L 52 " pdb=" CA SER L 52 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 604 0.052 - 0.105: 135 0.105 - 0.157: 27 0.157 - 0.210: 0 0.210 - 0.262: 1 Chirality restraints: 767 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C2 MAN B 4 " pdb=" C1 MAN B 4 " pdb=" C3 MAN B 4 " pdb=" O2 MAN B 4 " both_signs ideal model delta sigma weight residual False 2.52 2.66 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA VAL L 39 " pdb=" N VAL L 39 " pdb=" C VAL L 39 " pdb=" CB VAL L 39 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 764 not shown) Planarity restraints: 874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " 0.001 2.00e-02 2.50e+03 1.61e-02 3.23e+00 pdb=" CG ASN A 329 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " -0.016 2.00e-02 2.50e+03 pdb=" C1 NAG A 503 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 126 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " 0.005 2.00e-02 2.50e+03 9.49e-03 9.00e-01 pdb=" CG ASN A 329 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.006 2.00e-02 2.50e+03 ... (remaining 871 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 107 2.64 - 3.21: 4308 3.21 - 3.77: 8010 3.77 - 4.34: 11814 4.34 - 4.90: 19472 Nonbonded interactions: 43711 Sorted by model distance: nonbonded pdb=" NE ARG A 403 " pdb=" OE1 GLN A 432 " model vdw 2.080 3.120 nonbonded pdb=" OG SER A 331 " pdb=" O7 NAG A 503 " model vdw 2.147 3.040 nonbonded pdb=" OG SER A 219 " pdb=" OD2 ASP A 251 " model vdw 2.220 3.040 nonbonded pdb=" ND2 ASN H 56 " pdb=" O TYR A 284 " model vdw 2.252 3.120 nonbonded pdb=" O SER H 82B" pdb=" OG SER H 82B" model vdw 2.256 3.040 ... (remaining 43706 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=0.39 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: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 0.076 5027 Z= 0.196 Angle : 0.660 12.864 6856 Z= 0.324 Chirality : 0.046 0.262 767 Planarity : 0.003 0.040 870 Dihedral : 18.429 115.131 1920 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.85 % Allowed : 22.01 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.81 (0.34), residues: 616 helix: -0.15 (2.39), residues: 6 sheet: -0.23 (0.34), residues: 223 loop : -0.71 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 81 TYR 0.013 0.001 TYR A 121 PHE 0.011 0.002 PHE A 354 TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 5008) covalent geometry : angle 0.63940 ( 6810) SS BOND : bond 0.00334 ( 11) SS BOND : angle 1.81967 ( 22) hydrogen bonds : bond 0.21383 ( 160) hydrogen bonds : angle 9.31404 ( 441) link_ALPHA1-2 : bond 0.00465 ( 1) link_ALPHA1-2 : angle 1.68503 ( 3) link_ALPHA1-3 : bond 0.00181 ( 1) link_ALPHA1-3 : angle 1.56760 ( 3) link_BETA1-4 : bond 0.00316 ( 2) link_BETA1-4 : angle 1.87391 ( 6) link_NAG-ASN : bond 0.00152 ( 4) link_NAG-ASN : angle 2.72842 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.128 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 26 residues processed: 86 average time/residue: 0.3311 time to fit residues: 30.1477 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 431 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.0170 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.089717 restraints weight = 5759.032| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.24 r_work: 0.2941 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5027 Z= 0.129 Angle : 0.583 7.960 6856 Z= 0.304 Chirality : 0.046 0.210 767 Planarity : 0.004 0.043 870 Dihedral : 12.161 102.597 894 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.48 % Allowed : 20.34 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.74 (0.33), residues: 616 helix: -1.57 (1.71), residues: 7 sheet: -0.01 (0.34), residues: 222 loop : -0.75 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.016 0.001 TYR A 121 PHE 0.018 0.002 PHE A 132 TRP 0.011 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5008) covalent geometry : angle 0.57388 ( 6810) SS BOND : bond 0.00452 ( 11) SS BOND : angle 0.62053 ( 22) hydrogen bonds : bond 0.04509 ( 160) hydrogen bonds : angle 7.30775 ( 441) link_ALPHA1-2 : bond 0.00465 ( 1) link_ALPHA1-2 : angle 1.57008 ( 3) link_ALPHA1-3 : bond 0.01222 ( 1) link_ALPHA1-3 : angle 1.83435 ( 3) link_BETA1-4 : bond 0.00486 ( 2) link_BETA1-4 : angle 1.78012 ( 6) link_NAG-ASN : bond 0.00152 ( 4) link_NAG-ASN : angle 1.80098 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 430 ARG cc_start: 0.8375 (mmt90) cc_final: 0.8047 (mpt90) outliers start: 24 outliers final: 15 residues processed: 88 average time/residue: 0.3546 time to fit residues: 32.9405 Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 38 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN L 27BASN A 131 GLN A 141 ASN A 347 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.087079 restraints weight = 5780.446| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.22 r_work: 0.2901 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5027 Z= 0.209 Angle : 0.620 9.025 6856 Z= 0.320 Chirality : 0.047 0.209 767 Planarity : 0.004 0.044 870 Dihedral : 11.151 94.655 869 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.66 % Allowed : 21.08 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.82 (0.33), residues: 616 helix: -1.52 (1.70), residues: 7 sheet: -0.15 (0.33), residues: 222 loop : -0.75 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.017 0.002 TYR A 121 PHE 0.012 0.002 PHE A 354 TRP 0.013 0.002 TRP A 178 HIS 0.004 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 5008) covalent geometry : angle 0.60680 ( 6810) SS BOND : bond 0.00286 ( 11) SS BOND : angle 1.27074 ( 22) hydrogen bonds : bond 0.04207 ( 160) hydrogen bonds : angle 7.03325 ( 441) link_ALPHA1-2 : bond 0.00352 ( 1) link_ALPHA1-2 : angle 1.55645 ( 3) link_ALPHA1-3 : bond 0.00791 ( 1) link_ALPHA1-3 : angle 1.82896 ( 3) link_BETA1-4 : bond 0.00330 ( 2) link_BETA1-4 : angle 1.75544 ( 6) link_NAG-ASN : bond 0.00196 ( 4) link_NAG-ASN : angle 2.24894 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 304 ASP cc_start: 0.8336 (m-30) cc_final: 0.8108 (m-30) REVERT: A 430 ARG cc_start: 0.8311 (mmt90) cc_final: 0.7960 (mpt90) outliers start: 25 outliers final: 18 residues processed: 87 average time/residue: 0.3955 time to fit residues: 36.2481 Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 91 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.117860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.087616 restraints weight = 5783.798| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.21 r_work: 0.2912 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5027 Z= 0.182 Angle : 0.612 9.728 6856 Z= 0.314 Chirality : 0.047 0.206 767 Planarity : 0.003 0.043 870 Dihedral : 10.277 88.532 867 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.04 % Allowed : 20.71 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.85 (0.33), residues: 616 helix: -1.59 (1.65), residues: 7 sheet: -0.19 (0.33), residues: 222 loop : -0.76 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.015 0.001 TYR A 121 PHE 0.012 0.002 PHE A 354 TRP 0.013 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 5008) covalent geometry : angle 0.59648 ( 6810) SS BOND : bond 0.00281 ( 11) SS BOND : angle 1.35317 ( 22) hydrogen bonds : bond 0.03835 ( 160) hydrogen bonds : angle 6.84268 ( 441) link_ALPHA1-2 : bond 0.00394 ( 1) link_ALPHA1-2 : angle 1.55338 ( 3) link_ALPHA1-3 : bond 0.00969 ( 1) link_ALPHA1-3 : angle 1.81264 ( 3) link_BETA1-4 : bond 0.00279 ( 2) link_BETA1-4 : angle 1.84887 ( 6) link_NAG-ASN : bond 0.00159 ( 4) link_NAG-ASN : angle 2.36559 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 304 ASP cc_start: 0.8296 (m-30) cc_final: 0.8011 (m-30) REVERT: A 430 ARG cc_start: 0.8290 (mmt90) cc_final: 0.7785 (mmm160) outliers start: 27 outliers final: 20 residues processed: 88 average time/residue: 0.3602 time to fit residues: 33.3754 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 91 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.088310 restraints weight = 5851.313| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.27 r_work: 0.2918 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5027 Z= 0.162 Angle : 0.597 10.424 6856 Z= 0.304 Chirality : 0.047 0.200 767 Planarity : 0.003 0.043 870 Dihedral : 9.478 80.340 866 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.41 % Allowed : 20.34 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.85 (0.33), residues: 616 helix: -1.62 (1.59), residues: 7 sheet: -0.18 (0.33), residues: 222 loop : -0.76 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.015 0.001 TYR A 121 PHE 0.012 0.002 PHE A 354 TRP 0.013 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5008) covalent geometry : angle 0.58177 ( 6810) SS BOND : bond 0.00227 ( 11) SS BOND : angle 1.05023 ( 22) hydrogen bonds : bond 0.03600 ( 160) hydrogen bonds : angle 6.69403 ( 441) link_ALPHA1-2 : bond 0.00406 ( 1) link_ALPHA1-2 : angle 1.57149 ( 3) link_ALPHA1-3 : bond 0.01034 ( 1) link_ALPHA1-3 : angle 1.74137 ( 3) link_BETA1-4 : bond 0.00365 ( 2) link_BETA1-4 : angle 1.86787 ( 6) link_NAG-ASN : bond 0.00176 ( 4) link_NAG-ASN : angle 2.50606 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 142 ASN cc_start: 0.7873 (t0) cc_final: 0.7671 (t160) REVERT: A 304 ASP cc_start: 0.8291 (m-30) cc_final: 0.8002 (m-30) outliers start: 29 outliers final: 19 residues processed: 87 average time/residue: 0.3779 time to fit residues: 34.5181 Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN H 101 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.087080 restraints weight = 5890.154| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.23 r_work: 0.2897 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5027 Z= 0.208 Angle : 0.624 10.778 6856 Z= 0.316 Chirality : 0.047 0.208 767 Planarity : 0.004 0.045 870 Dihedral : 9.013 70.305 862 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.22 % Allowed : 21.08 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.89 (0.33), residues: 616 helix: -1.58 (1.60), residues: 7 sheet: -0.21 (0.33), residues: 222 loop : -0.78 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 81 TYR 0.016 0.002 TYR A 121 PHE 0.013 0.002 PHE A 354 TRP 0.013 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 5008) covalent geometry : angle 0.60728 ( 6810) SS BOND : bond 0.00277 ( 11) SS BOND : angle 0.89621 ( 22) hydrogen bonds : bond 0.03733 ( 160) hydrogen bonds : angle 6.72688 ( 441) link_ALPHA1-2 : bond 0.00354 ( 1) link_ALPHA1-2 : angle 1.62401 ( 3) link_ALPHA1-3 : bond 0.00863 ( 1) link_ALPHA1-3 : angle 1.91134 ( 3) link_BETA1-4 : bond 0.00279 ( 2) link_BETA1-4 : angle 1.94384 ( 6) link_NAG-ASN : bond 0.00246 ( 4) link_NAG-ASN : angle 2.83832 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7524 (ptt-90) REVERT: A 304 ASP cc_start: 0.8291 (m-30) cc_final: 0.8004 (m-30) outliers start: 28 outliers final: 20 residues processed: 87 average time/residue: 0.3810 time to fit residues: 34.8818 Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 57 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 45 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN H 101 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.090905 restraints weight = 5745.147| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.21 r_work: 0.2964 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5027 Z= 0.121 Angle : 0.577 10.629 6856 Z= 0.291 Chirality : 0.045 0.176 767 Planarity : 0.003 0.041 870 Dihedral : 7.900 57.934 862 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.48 % Allowed : 21.64 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.76 (0.33), residues: 616 helix: -1.48 (1.64), residues: 7 sheet: -0.14 (0.33), residues: 227 loop : -0.69 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.013 0.001 TYR A 121 PHE 0.013 0.001 PHE A 354 TRP 0.012 0.001 TRP A 178 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5008) covalent geometry : angle 0.55958 ( 6810) SS BOND : bond 0.00156 ( 11) SS BOND : angle 0.66825 ( 22) hydrogen bonds : bond 0.03286 ( 160) hydrogen bonds : angle 6.46098 ( 441) link_ALPHA1-2 : bond 0.00505 ( 1) link_ALPHA1-2 : angle 1.50630 ( 3) link_ALPHA1-3 : bond 0.01182 ( 1) link_ALPHA1-3 : angle 1.36101 ( 3) link_BETA1-4 : bond 0.00464 ( 2) link_BETA1-4 : angle 1.79454 ( 6) link_NAG-ASN : bond 0.00090 ( 4) link_NAG-ASN : angle 2.95574 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 304 ASP cc_start: 0.8288 (m-30) cc_final: 0.8010 (m-30) REVERT: A 430 ARG cc_start: 0.8306 (mmt90) cc_final: 0.8067 (mpt90) outliers start: 24 outliers final: 16 residues processed: 94 average time/residue: 0.4247 time to fit residues: 41.8091 Evaluate side-chains 86 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.086834 restraints weight = 5833.540| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.22 r_work: 0.2899 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5027 Z= 0.228 Angle : 0.630 9.034 6856 Z= 0.321 Chirality : 0.047 0.193 767 Planarity : 0.004 0.045 870 Dihedral : 7.790 58.631 861 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.48 % Allowed : 23.13 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.87 (0.32), residues: 616 helix: -1.31 (1.70), residues: 7 sheet: -0.23 (0.33), residues: 222 loop : -0.75 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.016 0.002 TYR A 121 PHE 0.013 0.002 PHE A 354 TRP 0.013 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 5008) covalent geometry : angle 0.60622 ( 6810) SS BOND : bond 0.00313 ( 11) SS BOND : angle 1.13587 ( 22) hydrogen bonds : bond 0.03758 ( 160) hydrogen bonds : angle 6.64381 ( 441) link_ALPHA1-2 : bond 0.00315 ( 1) link_ALPHA1-2 : angle 1.65253 ( 3) link_ALPHA1-3 : bond 0.00640 ( 1) link_ALPHA1-3 : angle 1.82065 ( 3) link_BETA1-4 : bond 0.00317 ( 2) link_BETA1-4 : angle 1.98892 ( 6) link_NAG-ASN : bond 0.00316 ( 4) link_NAG-ASN : angle 3.48949 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7543 (ptt-90) REVERT: H 82 SER cc_start: 0.8320 (t) cc_final: 0.7950 (p) REVERT: L 72 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.8085 (t) REVERT: A 85 ARG cc_start: 0.8401 (mtt180) cc_final: 0.8130 (mtt180) REVERT: A 140 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8665 (tp) REVERT: A 304 ASP cc_start: 0.8302 (m-30) cc_final: 0.8035 (m-30) outliers start: 24 outliers final: 21 residues processed: 82 average time/residue: 0.4350 time to fit residues: 37.4604 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN H 101 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.089510 restraints weight = 5775.789| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.20 r_work: 0.2936 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5027 Z= 0.147 Angle : 0.582 7.470 6856 Z= 0.298 Chirality : 0.046 0.158 767 Planarity : 0.003 0.043 870 Dihedral : 7.281 57.898 861 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.92 % Allowed : 23.69 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.79 (0.33), residues: 616 helix: -1.27 (1.72), residues: 7 sheet: -0.23 (0.33), residues: 227 loop : -0.66 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.014 0.001 TYR A 121 PHE 0.013 0.002 PHE A 354 TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5008) covalent geometry : angle 0.56097 ( 6810) SS BOND : bond 0.00216 ( 11) SS BOND : angle 0.85728 ( 22) hydrogen bonds : bond 0.03430 ( 160) hydrogen bonds : angle 6.50047 ( 441) link_ALPHA1-2 : bond 0.00458 ( 1) link_ALPHA1-2 : angle 1.57866 ( 3) link_ALPHA1-3 : bond 0.01030 ( 1) link_ALPHA1-3 : angle 1.51327 ( 3) link_BETA1-4 : bond 0.00436 ( 2) link_BETA1-4 : angle 1.90206 ( 6) link_NAG-ASN : bond 0.00172 ( 4) link_NAG-ASN : angle 3.23083 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: H 82 SER cc_start: 0.8332 (t) cc_final: 0.7951 (p) REVERT: A 85 ARG cc_start: 0.8385 (mtt180) cc_final: 0.8113 (mtt180) REVERT: A 140 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8596 (tp) REVERT: A 304 ASP cc_start: 0.8293 (m-30) cc_final: 0.8029 (m-30) outliers start: 21 outliers final: 16 residues processed: 86 average time/residue: 0.4105 time to fit residues: 37.2856 Evaluate side-chains 86 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 131 GLN A 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.085176 restraints weight = 5839.859| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.19 r_work: 0.2872 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 5027 Z= 0.303 Angle : 0.668 6.809 6856 Z= 0.345 Chirality : 0.049 0.189 767 Planarity : 0.004 0.047 870 Dihedral : 7.845 59.464 861 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.10 % Allowed : 23.51 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.97 (0.32), residues: 616 helix: -1.20 (1.72), residues: 7 sheet: -0.36 (0.33), residues: 222 loop : -0.78 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 81 TYR 0.017 0.002 TYR A 121 PHE 0.015 0.002 PHE H 78 TRP 0.015 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00688 ( 5008) covalent geometry : angle 0.64345 ( 6810) SS BOND : bond 0.00420 ( 11) SS BOND : angle 1.15317 ( 22) hydrogen bonds : bond 0.04080 ( 160) hydrogen bonds : angle 6.79531 ( 441) link_ALPHA1-2 : bond 0.00185 ( 1) link_ALPHA1-2 : angle 1.75616 ( 3) link_ALPHA1-3 : bond 0.00454 ( 1) link_ALPHA1-3 : angle 2.16379 ( 3) link_BETA1-4 : bond 0.00212 ( 2) link_BETA1-4 : angle 2.16836 ( 6) link_NAG-ASN : bond 0.00496 ( 4) link_NAG-ASN : angle 3.64595 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7511 (ptt-90) REVERT: H 82 SER cc_start: 0.8334 (t) cc_final: 0.7951 (p) REVERT: A 140 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8582 (tp) REVERT: A 304 ASP cc_start: 0.8303 (m-30) cc_final: 0.8020 (m-30) outliers start: 22 outliers final: 17 residues processed: 77 average time/residue: 0.4173 time to fit residues: 33.7821 Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN H 101 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.089137 restraints weight = 5813.890| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.23 r_work: 0.2932 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5027 Z= 0.152 Angle : 0.582 6.632 6856 Z= 0.301 Chirality : 0.046 0.143 767 Planarity : 0.003 0.043 870 Dihedral : 7.266 58.781 861 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.92 % Allowed : 23.69 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.83 (0.33), residues: 616 helix: -1.24 (1.75), residues: 7 sheet: -0.27 (0.33), residues: 227 loop : -0.68 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.014 0.001 TYR A 121 PHE 0.013 0.002 PHE A 354 TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5008) covalent geometry : angle 0.56351 ( 6810) SS BOND : bond 0.00223 ( 11) SS BOND : angle 0.78065 ( 22) hydrogen bonds : bond 0.03471 ( 160) hydrogen bonds : angle 6.55571 ( 441) link_ALPHA1-2 : bond 0.00403 ( 1) link_ALPHA1-2 : angle 1.58365 ( 3) link_ALPHA1-3 : bond 0.01018 ( 1) link_ALPHA1-3 : angle 1.49179 ( 3) link_BETA1-4 : bond 0.00379 ( 2) link_BETA1-4 : angle 1.92509 ( 6) link_NAG-ASN : bond 0.00175 ( 4) link_NAG-ASN : angle 2.99209 ( 12) =============================================================================== Job complete usr+sys time: 2156.48 seconds wall clock time: 37 minutes 28.52 seconds (2248.52 seconds total)